|
Dear All
I’m using distance restraints to force proper
orientation of the ligand in the active site of the receptor protein
(I’m investigating different binding modes).
I encountered a strange problem when defining distance restraints. I have protein and ligand topology combined in one itp file. At the end of this topology file (itp) I defined atoms pairs for distance restraints: …. [ distance_restraints ] ; ai aj type index type low up1 up2 fac 1384 4036 1 0 1 0.0 0.15 0.25 2.0 2957 4046 1 1 1 0.0 0.15 0.25 2.0 2957 4057 1 1 1 0.0 0.15 0.25 2.0 When looking at trajectory file I noticed that
restraints are present but not between defined atoms but probably between
pairs:
1383 4035
2956 4045 2956 4056 I checked the tpr file: gmxdump_mpi3 -s
posre100.tpr and I found that position restraints are not between defined pairs
but rather between
(atom-1,atom-1).
… Dis. Rest.: nr: 9 multinr[division over processors]: 9 9 9 9 9 9 9 9 9 9 9 9 … iatoms: 0 type=1244 (DISRES) 1383 4035 1 type=1245 (DISRES) 2956 4045 2 type=1245 (DISRES) 2956 4056 … Numbering of atoms in my topology file is correct
so I guess it’s not the case. What might be the problem. Am I doing
something wrong. I’m using gromacs3.3. Please give me comment on this
and thank you for help.
Best
regards
Michal |
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