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

Chris de Graaf degraaf at chem.vu.nl
Fri Aug 30 13:50:13 CEST 2002

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?

Thanks in advance and with kind regards,

Chris de Graaf

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