[gmx-users] Constraints - PMF - Different Molecules

Arthur Roberts aroberts99163 at yahoo.com
Tue Nov 18 00:26:30 CET 2008

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.

Steps running Gromacs 3.3.3:

1) Combine molecules A and B into a big structure file (i.e. pdb or  
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.
7) run grompp again to check this file to see if it is acceptable to  

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:

Torda, A. E., Scheek, R. M., and Gunsteren, W. F. v. (1989) Time- 
dependent distance restraints in molecular dynamics simulations, Chem.  
Phys. Lett. 157, 289-294.

I hope that helps.

On Nov 15, 2008, at 3:58 AM, Eudes Fileti wrote:

> Dear gmx-users, I need to use constraints between two
> polyatomic molecules in order to calculate PMF using free energy code.
> Can anybody help me to use these constraints over two different  
> molecules?
> I ve already read something in the forum but not helped me enough.
> (see http://www.gromacs.org/pipermail/gmx-users/2006-February/020049.html) 
> .
> bests
> eef
> _______________________________________
> Eudes Eterno Fileti
> Centro de Ciências Naturais e Humanas
> Universidade Federal do ABC
> Rua Santa Adélia, 166 - Bloco B, Sala 1048
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> skype: eefileti
> http://cromo.ufabc.edu.br/~fileti/
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