[gmx-users] distance restraint between 2 molecules

Catarina A. Carvalheda dos Santos c.a.c.dossantos at dundee.ac.uk
Wed Apr 27 09:09:09 CEST 2016

Hi Hong,

You have (at least) two options:

1) Edit the specbond.dat file so that the pdb2gmx creates a covalent bond
between the ligand and the protein (the bonded terms for this interaction
have to be present in the force field files);

2) Use position restrains on these two atoms instead.

Chose whatever makes more sense for your system.

Hope this helps.



Catarina A. Carvalheda
PhD Student
Computational Biology Division
University of Dundee
DD1 5EH, Dundee, Scotland, UK
Hi Gromacs users,
I want to assign a distance restraint between 2 atom, one belongs to
protein and one belongs to ligand. I have a .top file for protein and
include .itp of ligand. However, it seem Gromacs only perform distance
restraint between 2 atom within same molecule.
except the merging two molecules into a single moleculetype, is there any
option that i can keep protein and ligand itp files seperately?

Thank you so much.
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