[gmx-users] Re: itp file
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 11 17:54:17 CEST 2009
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 >
> 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 <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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