Subject: Re: CCL:neutral glycine in CHARMM ?

From: [email-masked] (Bob Funchess)
Date: Thu, 5 Feb 1998 18:41:49 GMT

Petr Belsky ([email-masked]) wrote:
> Dear netters,
> This is to ask how to build neutral glycine in CHARMM, it means
> NH2-CH2-COOH. We are working with CHARMM 23 and only zwitterion of
> glycine is present there.
> Many thanks in advance

> Petr Belsky
> [email-masked]

The easiest way is to apply the neutral terminus patches.  In MSI's version
those are COOH and NH2; I don't know off the top of my head if they're the
same for the academic version or not but you could look in the RTF file for
"PRES" records and see what's available there.

read sequ card
* Glycine
*
1
GLY

gene SEG1 setup
patch NH2  SEG1 1 setup
patch COOH SEG1 1 setup

--
Robert B. Funchess, Ph.D.                 [email-masked]
Senior Scientist, Scientific Support      Voice (619) 458-9990 x738
Molecular Simulations Inc.                FAX   (619) 458-0431
9685 Scranton Road
San Diego, CA 92121-3752                  http://www.msi.com/