Arthur Roberts wrote:
Dear Eudes,
You need to technically make it 1 "big molecule". As long as there are
no bonds specified between molecule A and B. The big molecule will
behave as if there are two molecules in it. I do it to dock small
molecules to proteins.
That's a good description, Arthur, thanks.
1) Combine molecules A and B into a big structure file (i.e. pdb or gro).
2) Edit this file, so that they are the same chain.
3) run pdb2gmx
4) Change all the residue names to MOL and change Protein_A to MOL in
the top and pdb files.
5) Make sure that there is no bonds between molecule A and B in the top
file. There probably won't be, but it is good to check anyway.
5) run grompp to check this file to see if it is acceptable to gromacs.
6) add distance restraints after the improper dihedrals. If you put it
anywhere else, it will not work.
That contradicts the description of the topology file format on (e.g.)
page 109 of the GROMACS 4 manual - "starting with GROMACS 3.1.3 all
directives at the parameter level can be used multiple times and there
are no restrictions on the order, except that an atom type must be
defined before it can be used in other definitions."
7) run grompp again to check this file to see if it is acceptable to gromacs
Other advise:
1) I would roughly dock the molecules together, so that you don't have
to have such a large water box.
2) I would experiment with force constants and time constants for the
distance restraints. A useful article is:
Mark
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