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
available.
> 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: case.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
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Received on Wed Apr 23 2003 - 23:53:01 PDT
