[gmx-users] Re: Distance restraints

Erik Lindahl lindahl at stanford.edu
Fri Feb 7 02:31:03 CET 2003

On Thursday, Feb 6, 2003, at 17:21 US/Pacific, Dmytro wrote:

> I already find an answer in mailing list, but some idea is steel not 
> clear to me.
> If I have two subunits each off 100 residue, in that case I should 
> combine their itp
> files and renumber  topology numbers of atoms from  the second chain 
> that they
> shold follow the first chain atoms numbers, consistent with gro file?
> Do I undestand correctly?
> But it is quite long procedure!
> Does anyone has a script for this?
> Dima

Hi Dima,

If they are separate molecules you do not need to do anything at all; 
just include both
files and list the molecules in the system section. For a reference, 
see how e.g. water
and protein molecules coexist in the topology.

If the two units are monomers of a polymer you should add them to the 
RTP database
file, and pdb2gmx will do everything automatically for you.



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