[gmx-users] protein membrane simulation
lopezmai at gmail.com
Wed Apr 4 21:39:57 CEST 2007
I´m working on membrane peptides simulation under lipid (POPC, from
Peter Tieleman group site). I downloaded the popc.pdb and lipid.itp
file from this site and i want to use the ffG53a5 force field. Some
days ago suggest to me i should to do something like this :
These are the steps i followed:
1. Added [atomtypes] from lipid.itp to ffG53a5nb.itp and to ffG53a5.atp
2. Added [pairtypes] from lipid.itp to ffG53a5nb.itp and removed any
with reference to HW as it will be zero regardless.
3. Added [dihedraltypes] from lipid.itp to ffG53a5bon.itp.
My popc128.top file is:
; Include forcefield parameters
; Include water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
[ system ]
POPC128 + 2460 water
[ molecules ]
; name number
But when i run grompp it gives :
No such moleculetype POP
Could you help me?
Have somebody a script for deleting the water molecules between the
monolayers (this molecules are added with genbox command).
All comments are very appreciated.
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