FW: [gmx-users] position restraints

abdullah ahmed abdullah_renk_ahmed at hotmail.com
Thu Jun 3 15:40:51 CEST 2010


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"

; Include water topology
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; Include generic topology for ions
#include "ions.itp"

[ system ]
; Name

[ molecules ]
; Compound        #mols
Protein_A           1

Thanks again for your help,

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