On Thu, Mar 04, 2004, yonchen wrote:
>
> Thank you for your hints. I edited the original pdb file to make sure
> that atom names are unique and I tried to create a frcmod as following
> method.
>
> antechamber -i bsheettest.pdb -fi pdb -o bsheettest.prep -fo prepi
> parmchk -i bsheettest.prep -f prepi -o frcmod
>
First, why are you running antechamber for a peptide? Antechamber is designed
for molecules that are _not_ part of the standard databases. Furthermore,
you must give antechamber only one residue at a time, not a complete polymer.
> Welcome to LEaP!
> > loadamberparams frcmod
> > bsheettest = loadpdb bsheettest.pdb
If you _did_ want to go the antehcamber route, you would need to load the
bsheettest.prep file before using a loadpdb command.
....hope this helps....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 Thu Mar 04 2004 - 16:53:00 PST
