[gmx-users] Re: itp file
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 11 18:23:41 CEST 2009
Jamie Seyed wrote:
> 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
Charge groups, in general, should at least have integer charge (i.e.,
carboxylate in an ASP side chain), but yes, zero is generally good.
> the same number. I still get the same Note. Should I assigned the same
Each CH3 groups should be its own charge group. You should not have multiple
CH3 groups in the same charge group.
> 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??
No. You'd be making the problems worse. The note is very clear - charge groups
should have very few atoms to avoid cutoff artefacts. If you assign your whole
structure to a charge group, you will still get the same note. You have to take
a large structure, break it down into smaller pieces of unit charge, and make
those your charge groups.
Look at your largest charge group, figure out what's in it, and decompose it
into smaller functional groups. Don't make any of them bigger.
-Justin
> Thanks a lot/Jamie
>
> On Tue, Aug 11, 2009 at 11:54 AM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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. > > > > > >
>
> ------------------------------------------------------------------------
> > > > > > _______________________________________________ >
> gmx-users mailing list > gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > > > >> > > > > >>> > > > > >> > > >
>
> > > >>>> > > >
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at > http://www.gromacs.org/search >
> before posting! > Please don't post (un)subscribe > requests
> to the
> > list. Use the > www interface or send it to >
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
>
> > > > > > >> > > > > > >>> > > > > > > >> > > > > > >>>>. >
> > Can't
> post? Read > http://www.gromacs.org/mailing_lists/users.php >
> > > --
> > ======================================== > > 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 > >
> ======================================== > >
> _______________________________________________ > gmx-users
> mailing
> list > gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>> >
> > > >>
>
> > > > > >>> > > > > > >> > > > > >>>> > > > >
> http://lists.gromacs.org/mailman/listinfo/gmx-users > Please
> search
> the archive at > http://www.gromacs.org/search before >
> posting! >
> Please don't post (un)subscribe requests > to the > list. >
> Use the
> www > interface or send it to > gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> > > > > > >> > > > > >
> >>> >
>
> > > > > >> > > > > > >>>>. > > Can't post? Read >
> http://www.gromacs.org/mailing_lists/users.php > > > > --
> ======================================== > > 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 > >
> ======================================== >
> _______________________________________________ > gmx-users
> mailing
> list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>> >
> > > > >>
>
> > > > > >>> >
> http://lists.gromacs.org/mailman/listinfo/gmx-users >
> Please search the archive at > http://www.gromacs.org/search
> before
> > posting! > Please don't post (un)subscribe requests to the >
> list. > Use the www > interface or send it to >
> gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
>
> > > > > >> > > > > > >>>. > Can't post? Read >
> http://www.gromacs.org/mailing_lists/users.php > > > > --
> ======================================== > > 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 > >
> ======================================== >
> _______________________________________________ > gmx-users
> mailing
> list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>> >
> > > > >>
>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please
> search the archive at > http://www.gromacs.org/search before >
> posting! > Please don't post (un)subscribe requests to the
> list. >
> Use the www > interface or send it to
> gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> > > > > > >>. > Can't post?
>
> Read > http://www.gromacs.org/mailing_lists/users.php > > > > --
> ======================================== > > 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 > >
> ======================================== >
> _______________________________________________ > gmx-users
> mailing
> list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>> >
> > > >
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users > Please
> search
> the archive at http://www.gromacs.org/search before > posting! >
> Please don't post (un)subscribe requests to the list. Use the
> www >
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> > > >. > Can't post? Read
>
> http://www.gromacs.org/mailing_lists/users.php > > > > -- >
> ======================================== > > 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 > >
> ======================================== >
> _______________________________________________ > gmx-users
> mailing
> list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>> > >
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users > Please
> search
> the archive at http://www.gromacs.org/search before > posting! >
> Please don't post (un)subscribe requests to the list. Use the
> www >
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>> > . > Can't post? Read
>
> http://www.gromacs.org/mailing_lists/users.php > > --
> ======================================== 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
> ========================================
> _______________________________________________ gmx-users mailing
> list gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
>
> http://lists.gromacs.org/mailman/listinfo/gmx-users Please search
> the archive at http://www.gromacs.org/search before posting!
> Please
> don't post (un)subscribe requests to the list. Use the www
> interface
> or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>. Can't post? Read
>
> http://www.gromacs.org/mailing_lists/users.php
>
>
> --
> ========================================
>
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list