[gmx-users] Re: itp file

[Justin A. Lemkul]

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>> 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>>>
>         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>>> 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>>> 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>>>
>         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>>>
> 
>                 >> 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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================