attach your top to the list? or just send to me directly.
Yang Ye
Farid Sa'adedin wrote:
Dear Xavier and Yang Ye,
I have done what you suggested by adding it to the lipid itp and
modifying the mdp files, but I still get the same 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_L dopc.top > grompptByAm1'
Any other ideas would be greatly appreciated.
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]>:
Farid Sa'adedin wrote:
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
You should try to put this include at the end of the topology of your
lipid.itp.
not here !!
define = -DPOSRES_L (-D)POSRES_W
you got to check if you need the second (-D), I never remember.
if you actually want to constraint the water !!
then call
#ifdef POSRES_L
#include "/home/tripos/lipid/dopc/minidopc/POSRE_L.itp"
#endif
#ifdef POSRES_W
#include "/home/tripos/lipid/dopc/minidopc/POSRE_W.itp"
#endif
you have a ; character at the beginning of the line !!
--
----------------------------------
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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