[AMBER] force addions to avoid replacing specific solvent molecules by ions

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Thu, 7 Dec 2017 11:14:41 +0100

Dear Ambers,

This may be a rather trivial question but somehow the following issue is
not clear to me. The issue came up because recently, we had to load in
Leap structures that have already a large number of water molecules that
we'd like to exclude from being replaced by ions during the leap
procedures to add ions.

When using "addIons" or "addIonsRand", solvent molecules overlapping
with future ions positions are removed (replaced with ions). Now, if we
have a structure with a layer of solvent molecules that we want to keep,
how do we instruct the addions command to not replace those specific
solvent molecules ? If the PDB file with waters is loaded as a unit in
leap, will the entire unit be considered "solute" or will the waters in
the unit be labeled automatically as "solvent" ?

We know "addions2" does not replace solvent molecules and could be used
prior to solvation but still we would like to use "addions" or
"addIonsRand" after solvation ...

Thanks for clarifying this

Best wishes

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
AMBER mailing list
Received on Thu Dec 07 2017 - 02:30:01 PST
Custom Search