[gmx-users] Constraints - PMF - Different Molecules

Mark Abraham Mark.Abraham at anu.edu.au
Tue Nov 18 01:53:47 CET 2008

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:


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