On Thu, Sep 27, 2012 at 1:34 PM, Fabrício Bracht <bracht.iq.ufrj.br> wrote:
> Hello. I have read in the manual that, if one uses softcore it is not
> necessary to have the same number of atoms in the topology files (and
> coordinates also?). Does that mean that the number of solvent
> molecules can also be different? What I mean is. Is there a problem if
> the total number of atoms of the systems are different, but not only
> due to the atoms lacking in the perturbed state, but also because leap
> adds different number of solvent molecules for each structure (for the
> one containing the group of study and for the one lacking that
> particular group)?
>
No, you need the same number of solvent molecules. The only places that
can differ are the perturbed region, I think.
You can use ParmEd to strip waters from the topology file, though, to make
them match. (An alternative is to make PDBs and do it through LEaP)
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 27 2012 - 11:00:03 PDT
