AMBER Archive (2003)

Subject: Re: AMBER: Non-standard Residue

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 23 2003 - 13:31:44 CDT

On Wed, Jul 23, 2003, Ran Ye wrote:
> Here's the address of my 1CAG-am.pdb file:
>
> http://www.cs.colostate.edu/~ye/1CAG-am.pdb.txt

antechamber only does a single residue at a time. You need to give it
just a blocked HYP residue, get a prepi file, then hand-modify the prepi
file to remove the blocking groups. Then you load the resulting residue
into LEaP, and *then* load the pdb file for the whole protein.

It's not as hard as it sounds, but you probably need some general experience
with Amber using standard residues before doing this.

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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