AMBER Archive (2004)

Subject: Re: AMBER: Use tleap convert *.pdb file to *.top and *.crd file

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 04 2004 - 10:47:10 CST

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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