Re: How to use GLYCAM force field in AMBER

From: David A. Case <>
Date: Wed, 23 Apr 2003 14:51:30 -0700

On Tue, Apr 22, 2003, Peng Tao wrote:

> 1) How to use GLYCAM in xleap? Do I just need to load all the .prep files
> from GLYCAM?

Generically, you need to use "loadAmberPrep" to get the prep files read in.
You can use the "list" command to see that which residues are available; these
names need to match those in your pdb file.

You also need to use "loadAmberParams" to load in the parameter files, so that
the force field parameters needed by the residues in the sugars will be

> 2) How to apply GLYCAM force field in sander? I have no idea about this.

Sander doesn't know or care about what force field you are using. If you
can make the prmtop file succesfully in LEaP, then sander will get all it
needs to know from that.

...good luck..dac

David A. Case                     |  e-mail:
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            |
Received on Wed Apr 23 2003 - 23:53:01 PDT
Custom Search