[gmx-users] Re: itp file

Jamie Seyed jamie.seyed at gmail.com
Tue Aug 11 18:07:13 CEST 2009 

Hi Justin,
I read the section 4.6.2, so according to the section I should have groups
with 0 charge, so I assigned each ch3 (total charge=0) for cgnr the same
number. I still get the same Note. Should I assigned the same number for all
atoms to cgnr in the atom section of itp-file?? In this way my whole
molecule will consider as one group which indeed has a charge=0?? Is this
true??
Thanks a lot/Jamie

On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Jamie Seyed wrote:
>
>> Hi Justin,
>> Is there any information on the gmx-website that explains how I should do
>> that? Does the tip means I should separate my original structure and the
>> groups that I attached to it??/ Many Thanks/Jamie
>>
>>
> Please see the manual, section 4.6.2.  I don't know what you mean by
> separating your structure.
>
> -Justin
>
>   On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>    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 > 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 > > >> 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 > > >
>>     > > >>> 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 > > > > > >> > > >
>>     > > >>>> 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 > > > > > >> > > > > >
>>     >>> > > > > >> > > > > > >>>>> 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 > > > > > >> > > > > >>> > > > > > >>
>>     > > > > >>>> > > > > >> > > > > > >>> > > > >> > > > > > >>>>>> > >
>>    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 > > > > > >> > > > > >>> > > > >
>>     > >> > > > > >>>> > > > > >> > > > > >>> > > > > > >> > > > >
>>     >>>>>> 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 > > > >> > > > >
>>     >>> > > > > >> > > > > > >>>> > > > > > >> > > > > > >>> > > > > >
>>     >> > > > > > >>>>>> 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
>>     > > > > >> > > > > > >>> > > > >> > > > > > >>>> > > > > >> > > > >
>>     > >>> > > > >> > > > > > >>>>>> > > 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 > > > > >> > > > > >>> > > > > > >> > > > >
>>     >>>> > > > > >> > > > > >>> > > > > > >> > > > > >>>>>> > > > >>
>>    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> > > > | (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 > >
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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 >
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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
>>    <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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