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"
[ system ]
; name
DOPC in water
#ifdef POSRES
#include "/home/tripos/lipid/dopc/minidopc/posre.itp" in water
;#include "/home/tripos/lipid/dopc/minidopc/p2.itp" in water
#endif
[ molecules ]
; name number
DOPC 18
SOL 1463
Quoting Xavier Periole <[EMAIL PROTECTED]>:
[EMAIL PROTECTED] wrote:
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'
You have to be very carefull in the order that you include the
information into the
topology files.
Basically you should include the information of posre after tohe
topology with the
"ifdef" flag ...
AND the position restrain on water must not include all water molecules !
You define it for one molecule.
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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