[gmx-users] Re: itp file
Vitaly V. Chaban
vvchaban at gmail.com
Tue Aug 11 07:57:33 CEST 2009
I asked you to show the order of sections ([defaults], [atomtypes],
etc) as they go one after another after you added all the .itp files.
Now you gave me only the .top file file and I don't see what you have
in the itp.'s. Please make a list of sections like [defaults],
[atomtypes], [bonds], etc with respect to your .itp and look at the
sequence. Something will not be correct here.
On Tue, Aug 11, 2009 at 12:46 AM, Jamie Seyed<jamie.seyed at gmail.com> wrote:
> Dear Vitaly,
> topol.top: -------------
> #include "ffoplsaa.itp"
> #include "spce.itp"
> #include "c80ch3.itp"
> fullerene in water
> 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>
>> 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.
>> On Tue, Aug 11, 2009 at 12:34 AM, Jamie Seyed<jamie.seyed at gmail.com>
>> > 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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