[AMBER] deletion of one water molecule from .rst and prmtop files

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Fri, 8 Jul 2011 10:48:26 +0530

Hi All,
I am running the MD of my protein-ligand complex in presence of few
crystallized water molecules using Amber10 and AmberTools1.2. Now for some
analysis purpose, I want to *delete one crystallized water molecule from the
.rst and .prmtop file *( or more precisely, I want to make new .rst and
.prmtop files without information about one crystallized water molecule).
Is that possible to do so in Amber. I checked Ptraj and found that "delete"
command deletes bond, angle and dihedral from the existing files.

Please let me know if there is any way to do this stuff??

Thanks and Regards,
Hirdesh Kumar
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Received on Thu Jul 07 2011 - 22:30:03 PDT
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