AMBER Archive (2003)

Subject: Re: sander & prmtop file generated from antechamber input ?

From: David A. Case (case_at_scripps.edu)
Date: Mon Apr 07 2003 - 00:28:58 CDT

On Mon, Apr 07, 2003, sychen wrote:

> I have the similar problem on my ligand which has saccharide residues,
> and glycam_2000 frcmod contains some atom types, like "EC", "AC" that
> are not in lower case. So, should I transform them to lower case or
> is there any other resolution of this problem?

Transforming to lower case won't do any good. The LCPO algorithm used to
estimate surface areas only knows about certain atom types, and the glycam
atom types are not among them. You would have to figure out which regular
types are closest in size to EC and AC, and put those into the sander code.

..regards...dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================