VMD-L Mailing List
From: Massimiliano Porrini (mozz76_at_gmail.com)
Date: Fri Feb 28 2014 - 05:18:51 CST
I am optimising atomic charges (from water-interaction profile) of
a cationic (+1) molecule with ffTK of VMD and I quote below
what is stated at Pag. 2760, 1st column, of the related paper
(C.G. Mayne, J. Saam, K. Schulten, E. Tajkhorshid, J.C. Gumbart
J. Comput. Chem. 2013, DOI: 10.1002/jcc.23422.):
*To better approximate the bulk-phase, for polar target compounds
theQM-optimized distances are shifted by an offset of -0.2 Angs andthe
interaction energies are scaled by 1.16 (for neutral molecules
only),although both parameters can be adjusted by the user.*
Therefore, since the molecule I am parametrising is not neutral but a
I do not have to scale the interaction energies (that is Scale = 1.0).
What is not clear to me, from the paper statement, is whether
the QM-optimised distances do not need to be
offset by -0.2 Angs (in case of non-neutral molecules) either.
Thanks in advance.
-- Dr Massimiliano Porrini Institut Européen de Chimie et Biologie (IECB) CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN) 2, rue Robert Escarpit 33607 Pessac Cedex France http://www.iecb.u-bordeaux.fr/ Emails: m.porrini_at_iecb.u-bordeaux.fr M.porrini_at_ed.ac.uk maxp_at_iesl.forth.gr mozz76_at_gmail.com