[gmx-users] Re: itp file

Jamie Seyed jamie.seyed at gmail.com
Tue Aug 11 17:30:28 CEST 2009 

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

On Mon, Aug 10, 2009 at 9:31 PM, Justin A. Lemkul <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 > > > | (540) > > 231-9080 > >
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> 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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> -- ======================================== > > 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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> ======================================== > > 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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> ======================================== > > 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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> ======================================== 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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