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.se...@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 <vvcha...@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.se...@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.se...@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 <vvcha...@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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