From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Nov 01 2005 - 12:57:43 CST
Richard,
In your bond assignments in the top.inp file there is a place where you
have listed CL bonding to two other C atoms. Or something of that flavor.
Psfgen then reads the bond info and by default finds angles and dihedrals
for those bonds and puts those entries in the .psf file.
I would check the psf file for two bond entries for the Cl index number.
Regards
brian
PS
Its amazing that namd ever becaming popular without a email list hmmm...
On Tue, 1 Nov 2005, Richard Wood wrote:
> Hi all,
>
> I have a chlorinated tyrosine residue that I have
> created a topology for (I asked for help and no one
> responded, so I proceeded on my own), and I am now
> trying to run an energy minimization on my molecule.
> Of course, it asks for parameters, first for vdW
> parameters for Cl, then for a C-Cl bond, then for a
> C-C-Cl angle. All of these I put in my parameter
> file. Then, when I run my calculation, it asks for
> the parameters for a CA CL CA angle, of which there is
> no such thing! (Or maybe there is?) What do i do?
>
> Richard
>
>
>
> __________________________________
> Start your day with Yahoo! - Make it your home page!
> http://www.yahoo.com/r/hs
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
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