[gmx-users] position restraints

[Anton Feenstra]

Outi Maija Salo wrote:
> 
> Hi!
> 
> I was about to do a position restrained mdrun and grompp said:
> 
> Fatal error: [ file "backbone_B_fix.itp", line 3 ]:
>              Atom index (3712) in position_restraints out of bounds (1-1431)
> 
> I have one protein but in three parts (A/B/C) as there are some residues
> missing in between. topol_A/B/C.itp files each have atom numbers starting
> from
> number one even though in gro file the atom numbers are continuous from
> one up to 5000 something. Could this explain the problem? How can I change
> the numbers in itp files to be continuous with regard to each other? Or is
> there another way to solve the problem?

In Gromacs, position restraints are defined as a property of the
molecule. That means, they are part of the molecule type definition.
As your protein is split in three parts, it will be treated as three
separate molecules, each with its own internal atom numbering. You
will need to find the proper atom numbers for your parts B and C and
convert the position restraints file(s) accordingly. Additionally,
the position restraints sections must be included in the proper sequence
with the molecule type definitions of your parts A, B, and C.
If you for example have topol_A/B/C.itp and posre_A/B/C.itp, your .top
file should contain a sequence like:

#include topol_A.itp
#include posre_A.itp
#include topol_B.itp
#include posre_B.itp
#include topol_C.itp
#include posre_C.itp


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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