[gmx-users] Re: itp file

[Jamie Seyed]

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 coordinate file
does not match topology..." I should fix this one now!!  Thanks a lot/Jamie

On Mon, Aug 10, 2009 at 8:10 PM, Justin A. Lemkul <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>> 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>> 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>> 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>> 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>>
>>         >> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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