AMBER Archive (2004)

Subject: Re: AMBER: Atom type

From: Rhonda Torres (
Date: Wed Jan 07 2004 - 12:55:40 CST

Hi Lan,

> And one more question. After I got the top & crd files and quit from the xleap,
> when I run xleap again the atom type in the parmset, where I added the SO type
> last time, was changed back (no SO type again). Is that mean I need to edit the
> parmset each time when I modify the molecule containing SO type?

Yes. Each time you modify your molecule and are creating a prmtop file
that reflects that modification, you will have to go through the same
procedure (addAtomTypes, loadoff .lib, loadpdb, etc.)

> Must I load the lib file?

Near as I can tell, yes. The .lib file contains the connectivity, charge, etc.



Rhonda A. Torres
The Scripps Research Institute
Department of Molecular Biology
10550 N. Torrey Pines Rd. TPC 15
La Jolla, CA 92037

phone: (858) 784-9781
fax: (858) 784-8896
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