Re: [AMBER] Structured water molecules with leap

From: David A Case <>
Date: Mon, 13 Jun 2011 09:08:09 -0400

On Fri, Jun 10, 2011, Guenegou, Guillaume [ORDFR] wrote:

> I try something like the following input file but after some trials, I
> am sure the solvatation (solvateBox ...) removes my structured water
> molecules.

Can you say how you are sure of this? You have a very complex script, so I
suppose something funny could happen, but the code for the solvateBox command
really can only add waters, not get rid of things that are already there.

You might make a PDB file from "complex4" (before the solvate box command)
and check that it actually has exactly what you want. Then, load that
into the leap and try the solvateBox command.

In general, you should use loadMol2 commands to generate a library
description for ligands and cofactors, but then issue a single loadPdb
command on a file that has *all* of your coordinates (protein, cofactor,
ligand, waters); then issue the solvateBox and addIons commands.

...good luck...dac

AMBER mailing list
Received on Mon Jun 13 2011 - 06:30:02 PDT
Custom Search