Hi!
In your previous mail you mentioned:
The position restraints must belong to the [moleculetype] of
the species to be restrained. Once you #include a new molecule, you start a
new
[moleculetype] entry and the position restraints belong to it.
So I rechecked my .top file and found that [moleculetype] only occurs once.
Perhaps I have misunderstood you. So I added the top file below. I did not add
the contents of [atoms] [bonds] etc because I felt the mail would become
unnecessarily long.
; Include forcefield parameters
#include "ffoplsaa.itp"
[ moleculetype ]
; Name nrexcl
Protein_A 3
[ atoms ]
[ bonds ]
[ pairs ]
[ angles ]
[ dihedrals ]
[ dihedrals ]
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include water topology
#include "spc.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
[ molecules ]
; Compound #mols
Protein_A 1
Thanks again for your help,
Abdullah
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