[gmx-users] Re: itp file

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 11 03:31:04 CEST 2009



Jamie Seyed wrote:
> Dear  Justin,
> Thanks for your all valuable comments. Actually I got these 2 notes:
> -----------------------------------------------------------------------------------
> 
> NOTE 1 [file topol.top, line unknown]:
>   The largest charge group contains 24 atoms.
>   Since atoms only see each other when the centers of geometry of the charge
>   groups they belong to are within the cut-off distance, too large charge
>   groups can lead to serious cut-off artifacts.
>   For efficiency and accuracy, charge group should consist of a few atoms.
>   For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.
> 
> NOTE 2 [file md.mdp, line unknown]:
>   You are using a plain Coulomb cut-off, which might produce artifacts.
>   You might want to consider using PME electrostatics.
> 
> -------------------------------------------------
> 
> How I can trust my results specially for first one?? Many Thanks/Jamie
> 

You should define smaller charge groups.  The tip given in the note is useful.

As for note 2, never use cut-off for electrostatics.  It is not as reliable as PME.

-Justin

> 
> 
> On Mon, Aug 10, 2009 at 9:18 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Jamie Seyed wrote:
> 
>         The gro file:
>         -------------------------
>         GROtesk MACabre and Sinister
>          1836
>            12        C    1   1.311   1.563   0.994
>            12        C    2   1.220   1.635   1.079
>            12        C    3   1.092   1.565   1.081
>            12        C    4   1.108   1.449   0.996
>         .........
> 
>            12        H  118   1.438   1.092   1.244
>            12        H  119   1.413   1.098   1.426
>            12        H  120   1.291   1.033   1.329
>            2SOL     OW  121   0.569   1.275   1.165
>            2SOL    HW1  122   0.476   1.268   1.128
>            2SOL    HW2  123   0.580   1.364   1.209
> 
>         .......
> 
>          572SOL    HW2 1833   2.024   1.991   2.158
>          573SOL     OW 1834   2.290   2.286   2.382
>          573SOL    HW1 1835   2.320   2.214   2.320
>          573SOL    HW2 1836   2.251   2.246   2.465
>           2.64467   2.64467   2.64467
> 
>         -----------------------------------------
>          and itp-file:
> 
>         -----------------
> 
>         ; Include forcefield parameters
> 
>         [ moleculetype ]
>         ; Name            nrexcl
>         C60CH3                 3
> 
>         [ atoms ]
>         ;   nr       type  resnr residue  atom   cgnr     charge      
>         mass  typeB    chargeB      massB
>             1   opls_145      1      C60CH3      C      1          0    
>         12.011   ; qtot 0
>             2   opls_516      1      C60CH3      C      2          0    
>         12.011   ; qtot 0
>         .....
> 
>          
>           71    78    79    69     3  1.740000e+02  5.000000e+00
>          3.000000e+00  1.740000e+02  5.000000e+00  3.000000e+00
>           69    79    80     2     3  2.580000e+02  5.000000e+00
>          3.000000e+00  2.580000e+02  5.000000e+00  3.000000e+00
> 
>         [ system ]
>         ; Name
>         C60CH3
> 
>         [ molecules ]
>         ; Compound        #mols
>         C60CH3                 1
>         -----------------------------------------------
> 
>         Oh Ok now I understand that I should remove only one of the
>         [molecule]
> 
> 
>     The [ system ] and [ molecules ] directives *only* belong in the
>     system .top, never in an .itp file.  Remove both [ system ] and [
>     molecules ] from the .itp, and list the appropriate molecules in the
>     [ molecules ] directive of the .top only.
> 
>     -Justin
> 
>         sections in itp-file (right)??
> 
>         Thanks a lot/ Please let me know if still something is
>         missing.../Thanks/Jamie
> 
> 
>          On Mon, Aug 10, 2009 at 8:42 PM, Justin A. Lemkul
>         <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
> 
> 
> 
>            Jamie Seyed wrote:
> 
>                First I put 1000, but after editconf and genbox it has been
>                changed to 572. I only have 1 part with SOL 572...
> 
> 
>            I'm thoroughly confused.  There is no need to manually manipulate
>            these sections if you're allowing genbox, genion, etc to
>         manipulate
>            them for you.  Please post the following information to get a
>            resolution:
> 
>            1. Your .top file
>            2. Your molecule.itp file (you can delete out lines in the atoms,
>            bonds, dihedrals section so the file is not unnecessarily
>         long - I'm
>            really just interested in the other directives that may be
>         present)
> 
>            -Justin
> 
>                On Mon, Aug 10, 2009 at 8:36 PM, Justin A. Lemkul
>                <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
> 
> 
> 
>                   Jamie Seyed wrote:
> 
>                       Hi Justin,
> 
>                       Thanks again... . Actully I have a question: I
>         have 1836
>                atoms
>                       (572 water and 1 molecule with 120 atoms). In top
>         of my
>                file.gro
>                       I have 1836 and in topology in [molecules] I have
>         c60ch3
>                1; and
>                       SOL 572 which means the same as above. So how I should
>                change it
>                       to get rid of error...??/
> 
> 
>                   The above should be correct.  However, you then have
>         in your .top
>                   you posted earlier:
> 
> 
>                   [molecules]
>                   molecule   1
>                   SOL       1000
> 
>                   This section is probably the source of your problem.
>          Again, as I
>                   said before, there should only ever be one [ molecules ]
>                section in
>                   the .top file.  Sounds like you've got two.
> 
>                   -Justin
> 
>                       Thank you in advance.../Jamie
>                       On Mon, Aug 10, 2009 at 8:20 PM, Justin A. Lemkul
>                       <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>> wrote:
> 
> 
> 
>                          Jamie Seyed wrote:
> 
>                              Hi Justin,
>                              Oh yes. I had a line that include ff again
>         and I
>                deleted that
>                              (is that ok)? now I got a new error related to
>                "number of
>                              coordinates in
> 
> 
>                          That's more than OK, that's correct.  As Mark
>         pointed
>                out, there
>                          should only ever be one invocation of [
>         defaults ] in
>                a topology.
> 
> 
>                              coordinate file does not match topology..." I
>                should fix this
>                              one now!!                    Simple one to
>         fix.  Figure out where the duplicate or
>                missing
>                          molecules are within the topology.  I'm
>         guessing your
>                       molecule.itp
>                          was really a molecule.top, complete with [
>         defaults ], [
>                       system ],
>                          and [ molecules ] directive, right? None of these
>                should be
>                       present
>                          in an .itp file, only a .top.
> 
>                          -Justin
> 
>                              Thanks a lot/Jamie
> 
> 
>                              On Mon, Aug 10, 2009 at 8:10 PM, Justin A.
>         Lemkul
>                              <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>
>                              <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu> <mailto:jalemkul at vt.edu
>         <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>
>                       <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>                <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>         <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>>>> wrote:
> 
> 
>                                 Can you post the contents of
>         molecule.itp?  The
>                first
>                              #include for
>                                 the force field is likely not the problem;
>                you've probably
>                              #included
>                                 it again in molecule.itp.
> 
>                                 -Justin
> 
>                                 Jamie Seyed wrote:
> 
>                                     Dear all,
>                                     I have a topology contains line as
>         below. I
>                do not
>                       understand
>                                     what is wrong with it that I get an
>         error
>                                     -----------
>                                      Program grompp, Version 4.0.5
>                                      Source Code file: topio.c, line: 415
>                                      Fatal error:
>                                      Syntax error-File ffoplsaa.itp, line 18
>                                      last line read:
>                                      '[defaults]'
>                                      Invalid order for directive defaults
>                                     --------------
>                                     according to the page
>                                                      
>         http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>                                     I do not have twice default
>         section... SO I
>                do not
>                       know
>                              exactly
>                                     which files I should check... It says
>                topology and ff.
>                              Topology
>                                     that I am using in grompp is as
>         below and the
>                              ffoplsaa.itp has
>                                     only one default section...
>                                     Would you please help me to solve
>         the problem.
>                                     topol.top: -------------
>                                     #include "ffoplsaa.itp"
>                                     #include "spce.itp"
>                                     #include "molecule.itp"
>                                     [system]
>                                     fullerene in water
>                                     [molecules]
>                                     molecule   1
>                                     SOL       1000
>                                     --------------------
>                                     Many Thanks in Advance and I
>         appreciate your
>                       help/Jamie
> 
>                                      On Mon, Aug 10, 2009 at 5:46 PM,
>         Jamie Seyed
>                                     <jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>>
>                                     <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>>>>
> 
>                                     wrote:
> 
>                                        Dear Vitaly,
>                                        topol.top: -------------
>                                        #include "ffoplsaa.itp"
>                                        #include "spce.itp"
>                                        #include "c80ch3.itp"
>                                        [system]
>                                        fullerene in water
>                                        [molecules]
>                                        C80CH3   1
>                                        SOL       1000
>                                        --------------------
>                                        my command is:
>                                        grompp -f md.mdp -c f.gro -p
>         topol.top
>                -o pr.tpr
>                               -maxwarn 10
>                                            Thank you for helping me out to
>                solve the
>                       problem/
>                                     Regards/Jamie
>                                                On Mon, Aug 10, 2009 at
>         5:39 PM,
>                Vitaly
>                       V. Chaban
>                                        <vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>>
>                              <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>>>
>                                     <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>>>
>                              <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>>>>> wrote:
> 
>                                            Jamie,
> 
>                                            The idea is the same. Some
>         directive
>                is not
>                       at its
>                              place. I
>                                            cannot say
>                                            which is exactly because I
>         don't see
>                all the
>                              picture with
>                                     your
>                                            topology file (+included files).
>                Write the
>                       sequence of
>                                     directives as
>                                            they go in .top (+included
>         .itp) and
>                then
>                       we will see
>                                     what sections
>                                            must be shifted or maybe just
>         swapped.
> 
>                                            Vitaly
> 
>                                            On Tue, Aug 11, 2009 at 12:34
>         AM, Jamie
>                                            Seyed<jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>
>                                     <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
> 
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
> 
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
> 
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>
> 
>                                     <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>>>> wrote:
>                                             > Hi Vitaly,
>                                             > When I add it back, I got
>         the old
>                error
>                                             > -----------
>                                             > Program grompp, Version 4.0.5
>                                             > Source Code file: topio.c,
>         line: 415
>                                             > Fatal error:
>                                             > Syntax error-File
>         ffoplsaa.itp,
>                line 18
>                                             > last line read:
>                                             > '[defaults]'
>                                             > Invalid order for
>         directive defaults
>                                             > -----------
>                                             > Now do you have any idea??? I
>                appreciate
>                       your
>                              help/Jamie
>                                             >
>                                             > On Mon, Aug 10, 2009 at
>         5:22 PM,
>                Jamie Seyed
>                                            <jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>>
>                                     <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com> <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>
>                              <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com <mailto:jamie.seyed at gmail.com>>
>                       <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>
>                <mailto:jamie.seyed at gmail.com
>         <mailto:jamie.seyed at gmail.com>>>>>>>
> 
>                                     wrote:
>                                             >>
>                                             >> Hi Vitaly,
>                                             >> I did it because I read from
>                                             >>
>                                                                  
>          http://oldwiki.gromacs.org/index.php/Errors#Found_a_second_defaults_directive_file
>                                             >> that says:
>                                             >> "One solution is to simply
>                comment out
>                       (or delete)
>                                     the lines
>                                            of code out
>                                             >> in the file where it is
>         included
>                for the
>                              second time
>                                     i.e.,
>                                            ..". So if it is
>                                             >> the case I am going to
>         undo it
>                to see what
>                              happens...
>                                     I will
>                                            let you know.
>                                             >> Thanks/Jamie
>                                             >> On Mon, Aug 10, 2009 at
>         5:05 PM,
>                Vitaly
>                       V. Chaban
>                                            <vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>>>
>                              <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>>>
>                                     <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>>>
>                              <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>
>                       <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com> <mailto:vvchaban at gmail.com
>         <mailto:vvchaban at gmail.com>>
>                <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>
>         <mailto:vvchaban at gmail.com <mailto:vvchaban at gmail.com>>>>>>>
> 
> 
>                                             >> wrote:
>                                             >>>
>                                             >>> Why did you comment out
>                [defaults] in
>                              ffoplsaa.itp? The
>                                            general idea
>                                             >>> is that the sections in the
>                resulting
>                              topology file
>                                     (after
>                                            including
>                                             >>> #include's) must be
>         placed in the
>                       strict order.
> 
> 
> 
> 
>                                                      
>         ------------------------------------------------------------------------
> 
> 
> 
>                                    
>         _______________________________________________
>                                     gmx-users mailing list          
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>                <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
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>         <mailto:gmx-users at gromacs.org>
>                <mailto:gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>>>>>
> 
>                                          
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>         <mailto:gmx-users-request at gromacs.org>>>>
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>         <mailto:gmx-users-request at gromacs.org>>>
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> 
>                                     Can't post? Read
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> 
> 
>                                 --  
>          ========================================
> 
>                                 Justin A. Lemkul
>                                 Ph.D. Candidate
>                                 ICTAS Doctoral Scholar
>                                 Department of Biochemistry
>                                 Virginia Tech
>                                 Blacksburg, VA
>                                 jalemkul[at]vt.edu <http://vt.edu/>
>         <http://vt.edu/>
>                <http://vt.edu/> <http://vt.edu/>
>                       <http://vt.edu/> | (540)
> 
>                              231-9080
> 
>                                      
>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>                                 ========================================
>                                
>         _______________________________________________
>                                 gmx-users mailing list  
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> 
>                                 Can't post? Read
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> 
> 
> 
>                          --    ========================================
> 
>                          Justin A. Lemkul
>                          Ph.D. Candidate
>                          ICTAS Doctoral Scholar
>                          Department of Biochemistry
>                          Virginia Tech
>                          Blacksburg, VA
>                          jalemkul[at]vt.edu <http://vt.edu/>
>         <http://vt.edu/> <http://vt.edu/>
>                <http://vt.edu/> | (540)
>                       231-9080
>                        
>          http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>                          ========================================
>                          _______________________________________________
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> 
> 
> 
>                   --    ========================================
> 
>                   Justin A. Lemkul
>                   Ph.D. Candidate
>                   ICTAS Doctoral Scholar
>                   Department of Biochemistry
>                   Virginia Tech
>                   Blacksburg, VA
>                   jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/>
>         <http://vt.edu/> | (540)
>                231-9080
>                   http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>                   ========================================
>                   _______________________________________________
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> 
> 
>            --    ========================================
> 
>            Justin A. Lemkul
>            Ph.D. Candidate
>            ICTAS Doctoral Scholar
>            Department of Biochemistry
>            Virginia Tech
>            Blacksburg, VA
>            jalemkul[at]vt.edu <http://vt.edu/> <http://vt.edu/> | (540)
>         231-9080
>            http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>            ========================================
>            _______________________________________________
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> 
> 
> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     _______________________________________________
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> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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