[gmx-users] distance restraints in enzyme-substrate complex

[K.A. Feenstra]

Chris de Graaf wrote:
> 
> Dear gmx-people,
> 
> I want to optimize an enzyme-substrate complex using experimentally
> (spin-relaxation NMR) derived distance restraints between a heme-iron
> (part of the protein) and five H atoms of the ligand.
> 
> I made a conf.gro-file containing both the protein and the ligand (the
> latter included as a subsequent residue-number with subsequent atom
> numbering), an .mdp-file (disre = Simple), a topology file (with the
> distance restraints defined under "[ distance_restraints ]" and
> "#include "ligand.itp"" to refer to the file containing the topology for
> the ligand).
> 
> When  I want to make a tpr-file I receive the fatal error: "[ file
> "topol.top", line 29420 ]: Atom index (4755) in distance_restraints out
> of bounds (1-4748)". It must be stated that in the conf.gro file, atoms
> 1-4748 belong to the protein structure, while atoms 4749-4775 belong to
> the ligand. How can I solve this problem? Do I have to insert the
> topology of the ligand in the topol.top file explicitely (and adjust the
> atom numbering of the ligand), and/or is this error a result of the
> wrong placement of "[ distance_restraints ]" and  "#include
> "ligand.itp"" in the topol.top file?

Distance restraints can only be defined inside one molecule, which means
specifically that all atoms must be within one [ moleculetype ] section.
So, your suggestion to insert the ligand into the .top file and renumber
all atoms of the ligan, will work. 

This is a known, and severe, limitation but we have not (yet) found a 
satisfactory solution.

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
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