Hi,
I am trying to restrain an ion that is coordinated by a few protein
atoms, to avoid that the ion might fly off. The simulation should be run
on a GPU (with OpenMM) and implicit solvent. First I tried to restrain
the ion using bonds of type 6, but harmonic potentials are not supported
by OpenMM. Turning the restraint into a normal bond (type 1) would be
fine since I only constrain bond lengths of hydrogens. However, that
gives a grompp error,
"Cannot find length for atoms 386-2262 involved in angle"
meaning that the function find_gb_bondlength in topio.c does not find a
bond length for the ion-protein atom bond, although the bond length is
clearly defined in the topology.
I am a bit stuck now. Does anyone know how one could introduce some kind
of distance restraint with OpenMM and implicit solvent?
I am using gmx 4.5.3 and OpenMM 2.0.
Thanks a lot,
Jochen
--
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Dr. Jochen Hub
Computational and Systems Biology
Dept. of Cell& Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4715056 Fax: +46-18-511755
http://xray.bmc.uu.se/~jochen/index.html
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