Michal Kolinski wrote:
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
How did you tell this? If using gmxdump, then see below.
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
Array numbering in C starts with zero. PDB atom numbering starts with
one. pdb2gmx is just dumping the contents of arrays, without regard to
whether they correspond to atoms or not. Doing anything else would be
bizarre with respect to the conventions of C and programming in general.
Mark
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