[gmx-users] Re: itp file

Justin A. Lemkul jalemkul at vt.edu
Tue Aug 11 02:36:02 CEST 2009



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>> 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>>> 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>>>>
> 
>                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>>>> 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>>>> 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>>>>
> 
>                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>>>>
> 
> 
>                        >> 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.
> 
> 
> 
> 
>              
>          ------------------------------------------------------------------------
> 
> 
> 
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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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