[gmx-users] Re: itp file

[Justin A. Lemkul]

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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