[gmx-users] distance restraints problem

[Mark Abraham]

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