Re: [AMBER] residue split

From: David A Case <>
Date: Wed, 17 Oct 2012 09:19:14 -0400

On Wed, Oct 17, 2012, Carlos Romero wrote:
> pdb file i try to use is 3BEF. it's a thrombine molecule in complex with
> par-1.
> And respect to your observations, I think that yes, the first residue is
> something like 1A, 1B, etc.
> Please could you help me how can i edit my pdb file?

As long as the residue divisions printed out by LEaP look correct, you
probably don't need to do anything. Just be sure that there are not two
residues of the same type next to each other with variants of the same residue
number: (e.g. GLU 1C followed by GLU 1D). Check the duplicate atom messages
for things that are *not* alternate conformers in the original PDB file.

> I tried to use antechamber but it give many errors.

Antechamber should *only* be used to process single-residue PDB files. It
should indeed give lots of errors (hopefully with understandable messages) if
you try to give it a PDB file with more than one residue.

...good luck....dac

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Received on Wed Oct 17 2012 - 06:30:05 PDT
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