[gmx-users] distance restraints problem

[Jim Fonseca]

I believe that there's no problem with the numbering.  The numbering  
in the topology will start with 1, however due to Gromacs'  
implementation, the indexing starts at 0. So, atom 4036 in your .itp  
corresponds to 4035 in the trajectory file.  Note that if you look in  
your trajectory file you should see an atom indexed at 0. For example:
       x[    0]={ 9.82700e+00,  6.47400e+00,  1.01800e+01}

hth
Jim

On Mar 3, 2006, at 10:00 AM, 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
>
> 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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