AMBER: Re: dynamics of isolated system (fwd)

From: David A. Case <>
Date: Wed, 6 Aug 2003 14:43:29 -0700

On Tue, Aug 05, 2003, Dr. Yong Duan wrote:
> Date: Fri, 01 Aug 2003 11:17:35 -0300
> From: Herbert Georg <>
> Subject: Re: dynamics of isolated system
> The geometry was obtained by Molecular Mechanics optimization (something
> like the energy minimization that AMBER does when IMIN=1) with AMBER94
> parameters, using Hyperchem to be more specific.

Sorry I didn't pick up on this before....atom names within a residue must
be unique, this is a requirement of LEaP.

If I load a pdb file created from your prmtop/coord file into LEaP, I see
the following:

> x = loadpdb alphacd.pdb
Loading PDB file: ./alphacd.pdb
-- residue 1: duplicate [ C] atoms (total 36)
-- residue 1: duplicate [ H] atoms (total 60)
-- residue 1: duplicate [ O] atoms (total 30)

     (same-name atoms are reduced to a single atom)

This should be a fatal, rather than a non-fatal error (Scott??). But anyway,
you have to really pay attention to warnings like this.

To work around this, you need to make sure that each atom has a unique

...hope this helps...sorry I didn't pick up on this earlier....dac

David A. Case                     |  e-mail:
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:                   
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Received on Wed Aug 06 2003 - 22:53:00 PDT
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