[gmx-users] S(q) and polymer MD ?!?!

[Luciano Costa]

Dear gmx-users and dear Spoel,

I'm some time without to use the gromacs. Well, I did a system here with
polymer molecules, in which I insert force field paramters in the opls
files.

My topology file is:

; The force field files to be included
#include "ffoplsaa.itp"
#include "ffoplsaa_peo_bon.itp"
#include "ffoplsaa_peo_nb.itp"

; Include other molecules here (topology)
; eg. BMIM + PF6
#include "peo.itp"
#include "bmim.itp"
#include "pf6.itp"

[system]

PEO in ionic liquid

[molecules]
;molecule name          nr.
PEO                     30
BMIM                    100
PF6                     100

The peo.itp, bmim.itp and pf6.itp files are well defined, such as gromacs
guide. When I tried run the grompp program, it was shown the following
message:


creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
checking input for internal consistency...
calling /lib/cpp...
Tried to execute: '/lib/cpp  -I/usr/local/share/gromacs/top  peo.top >
gromppC93iHn'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
Cleaning up temporary file gromppC93iHn
Fatal error: Invalid order for directive bondtypes, file
""/usr/local/share/gromacs/top/ffoplsaa_peo_bon.itp"", line 4

##########################

I check this *.itp file and I didn't see nothing ... I don't get solve the
problem.
What should I do, please ?!


ABOUT S(q) using g_rdf I read a message about this here, but it not had the
answer about *.tps !!!! What is this file format and how can I do this
analysis in gromacs ?!?!

Well, very veyy thanks !!

Cheers,

Luciano


--
### Luciano Tavares da Costa ###
##       MSc. Eng. Químico
##       100 % Linux
#############################
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