Re: Re: Besides PSFGEN, (Thank you)

From: Shirley Li (
Date: Fri Dec 23 2005 - 17:42:54 CST

Hi Josh,
 Thanks a lot for the helpful information. That's really a nice alternative way.
"Joshua D. Moore" <> wrote: Hi Shirley,

I use the OPLS force field, so I actually do not have a topology file, and
I don't want to create one. I use Alessandro Pedretti's Vega ZZ to create
all my .psf files. I load in a .pdb FAT formatted file. It contains all
of the usual .pdb coordinate info and atom names, but it also contains
information about connectivity in the CONECT records as well as the
charges and atom types that link your .pdb file to your parameter file.
There is a nice description of this format in the manual found on the
webpage. I love it because I just build one .pdb FAT file for each
molecule I am using. Then I can replicate it on a lattice in VEGA ZZ and
simulate as many as I want.

Vega ZZ is free for academic use and can be downloaded for Windows at

It also has a lot of other useful tools, including a solvation tool which
allows you to solvate with anything. You can put in your own solvents.

You can save your .pdb (nonstandard with only the coordinate info which is
all NAMD needs) and the XPLOR formatted .psf file directly from Vega ZZ
and start your simulation.

Hope this helps.


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

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