Dear Xavier,
My posre.itp file represents one lipid molecule. My p1.itp represents
1 water molecule.
I made new itp files using genpr defining one lipid molecule and water
molecule called POSRE_L.itp and POSRE_W.itp as you suggested them to be
called.
The strange thing is that I can restrain the lipids when there is no
water in my system. But when I add water to the system, grompp doesn't
seem to restrain the lipids anymore. It brings up this message:
cpp exit code: 256
cpp: too many input files
[tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
-I/usr/local/share/gromacs/top
-DPOSRES dopc.top > grompptByAm1'
TOP FILE:
[ system ]
; name
DOPC in water
#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp" in water
;#include "/home/tripos/lipid/dopc/minidopc/POSRE_W.itp" in water
#endif
[ molecules ]
; name number
DOPC 18
SOL 1463
As you can see from my top file everything is in order. I define the
lipid and water seperately in the top file. But how can I define them
seperately in my mdp file?
Yours,
Farid
--
Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Summerhall
Edinburgh EH9 1QH
SCOTLAND
Quoting Xavier Periole <[EMAIL PROTECTED]>:
[EMAIL PROTECTED] wrote:
Dear Xavier,
I have put the posre.itp file in the order that you mentioned and I
have a file which has postional restraints on one water molecule.
(See previous email below) So it is not an ordering problem.
If anyone has any suggestions why grompp isn't restraining just the
lipid molecules in my bilayer/water system I would greatly
appreciate it.
The posre itp file represents one lipid molecule and the p2.itp file
represents all water molecules.
I have a p1.itp file that represents one water molecule but this
also brought up the :
cpp exit code: 256
cpp: too many input files
[tripos]dopc/minidopc$ Tried to execute: '/lib/cpp -I
-I/usr/local/share/gromacs/top
-DPOSRES dopc.top > grompptByAm1'
message.
TOP FILE:
#include "/home/tripos/lipid/ffgmx2_lipid.itp"
#include "/home/tripos/lipid/DOPCHT.itp"
#include "/usr/local/share/gromacs/top/spc.itp"
Did you try to define one POSRES flag for the water and one for the lipids.
I mean one call POSRE_W the other POSRE_L and then define
then in the mdp file and call them separatelly at their respective places ?
Not together, but in the itp of the lipid and itp of the water ?
XAvier
--
----------------------------------
Xavier Periole - Ph.D.
Dept. of Biophysical Chemistry / MD Group
Univ. of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Tel: +31-503634329
Fax: +31-503634398
email: [EMAIL PROTECTED]
web-page: http://md.chem.rug.nl/~periole
----------------------------------
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