Only atoms involved in the transformation can differ.
Solute and solvent atoms which are not involved must
be identical AND have identical coordinates. This makes
the building process a little more convoluted ... I definitely
suggest reading through the tutorial to orient yourself with
the process.
http://ambermd.org/tutorials/advanced/tutorial9/
--Niel
________________________________________
From: Fabrício Bracht [bracht.iq.ufrj.br]
Sent: Thursday, September 27, 2012 11:34 AM
To: AMBER Mailing List
Subject: [AMBER] TI and number of solvent molecules
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)?
Thank you
Fabrício
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Received on Thu Sep 27 2012 - 11:00:04 PDT
