The structure of the topology shall be
#include "ff"
;Beginning of molecule definition 1
[ moleculetype ] -\
Mol1 |
|---This is in one itp file
[ atoms ] |
... -/
[ position_restraints ] ; ---This normally in another itp file.
;End of molecule definition 1
;Begin of Molecule definition 2
...
;End of molecule definition 2
[ system ]
; name
ABC
[ molecules ]
; name number
Mol1 1
Mol2 1
Yang Ye
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
[ 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
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