Re: [AMBER] Problem with PDB files in LEaP

From: David A Case <>
Date: Fri, 28 Jun 2013 13:19:53 -0400

On Fri, Jun 28, 2013, Hunter Brown wrote:
> This is concerning, because there are a lot of errors and warnings in my
> simple test of the RCSB file. The grad student I am working with said
> that for my large solvated/ionized system I should be getting no errors,
> and only a handful of warnings.

In addition to Dan's careful analysis, see section 6.8 of the AmberTools13
Manual, which goes over many of the things you need to look at in a PDB file
before feeding it to Amber. RSCB files have all kinds of things in them,
and one generally needs to do some editing before proceeding with LeAP.

[Dan: can you put your detailed explanation of common LEaP problems into the


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Received on Fri Jun 28 2013 - 10:30:02 PDT
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