[gmx-users] distance restraint between 2 molecules

[Erik Marklund]

Hi,

Or use the pull code.

Kind regards,
Erik
 
> On 27 Apr 2016, at 08:09, Catarina A. Carvalheda dos Santos <c.a.c.dossantos at dundee.ac.uk> wrote:
> 
> 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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