[gmx-users] distance restraints problem

[Michal Kolinski]

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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