[gmx-users] Re: itp file
Justin A. Lemkul
jalemkul at vt.edu
Tue Aug 11 02:42:36 CEST 2009
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 <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto: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>>
> <mailto: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>>>
> <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
> <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>>>
> <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 <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>>> <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
> <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>>>
> <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
> <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>>>
> <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 <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/>
> <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/> <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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