Re: [AMBER] Protein, Water and Amber

From: <>
Date: Mon, 8 Mar 2010 03:54:59 -0500 (EST)

Hi Imtiaz,

> I am running a solvated protein simulation also keeping all the waters
> molecule of the original PDB file. Is there anyway/script or VMD command
> that I can distinguish original waters (in PDB) from the solvent waters
> (added by tleap) in VMD.

Normally, leap will build your unit sequentially, so your protein&ligand
residues should come first, then all waters and salts that were in the
original structure, followed by the water molecules that leap added for
you. Just check the residue numbering and count how many X-ray waters you
had, then select the first N waters by resid in vmd.

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Mon Mar 08 2010 - 01:00:02 PST
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