From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Tue Jul 26 2005 - 20:55:03 CDT
I don't know how to do this in VMD, but you can easily do this with Vega ZZ
http://www.ddl.unimi.it/vega/index.htm
I don't see CCl4 as a solvation cluster in the download, but Vega ZZ
allows you to add your own solvation clusters. I have used this to
solvate with SPC/E water to use in NAMD. You will have to give it a PDB
FAT formatted file of the CCl4 solvation cluster. This is a format that
includes the coordinates, connectivity, and the charge information
(normally included in the PSF file). There is a very nice online user
manual which describes this format if you have questions.
Vega ZZ will write your needed PSF and PDB files as well once you have
solvated.
Josh
On Tue, July 26, 2005 9:37 am, Jack wrote:
> Hi all,
>
> Does anyone know how to solvete a compound (e.g. peptide) in CCl4 using
> VMD?
> Thanks in advance.
>
> Jack
>
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Joshua D. Moore
Graduate Student
North Carolina State University
Department of Chemical and Biomolecular Engineering
Box 7905 Centennial Campus
Engineering Building I
911 Partners Way
Raleigh, NC 27695-7905
Phone: (919) 513-2051
Fax: (919) 513-2470
Email: jdmoore_at_unity.ncsu.edu
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