[gmx-users] Re: itp file

[Jamie Seyed]

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> 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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