Mark Abraham wrote:
Thanks Mark for your advice
I tried to run the simulation even by removing all the restraints as you
told but the same problem was coming.
In your second reply you asked me to check the topology file. I have a
doubt in that, actually what are the things i should look at in the
topology
file. I have seen my topology file and the related .itp files also but i
did
not find anything unusual in that.
Following are the contents of my Topology file:
; Include forcefield parameters
#include "ffG43a1.itp"
; Include chain topologies
#include "aquapomut_grom_A.itp"
#include "aquapomut_grom_B.itp"
; Include water topology
#include "spce.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include generic topology for ions
#include "ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
Protein_A 1
Protein_B 1
SOL 71
CL- 6
SOL 14825
Two regions of SOL doesn't sound like a good idea, but I won't swear it's
the problem.
this is why I suggested grompp -maxwarn 0, because it will detect the
inconsistencies in names and tell you to fix it.
Mark
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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