[gmx-users] Re: itp file

[Mark Abraham]

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... 

grompp thinks you do. Check the contents of all the files you #include. 
See http://oldwiki.gromacs.org/index.php/include_file_mechanism for 
explanations. As explained on the link you provided, only your 
forcefield .itp file has any business using this directive.

Mark

> 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> 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>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>
>>> 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>
>>> 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>
>>>>> 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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