[gmx-users] distance restraint between 2 molecules

[Catarina A. Carvalheda dos Santos]

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.

Regards,

-- 

Catarina A. Carvalheda
PhD Student
Computational Biology Division
SLS & SSE
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.
Hongtham
--
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