AMBER Archive (2009)

Subject: Re: AMBER: bug of the mm_pbsa module in ambertools 1.2

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Tue Jan 06 2009 - 12:59:15 CST

Hi,

On Mon, 5 Jan 2009, Ye Mei wrote:

> Here I report a bug I have found in the the mm_pbsa module in ambertools 1.2.
> Some atoms may have their names changed when generating the pdb file for delphi. For example, H3 may be renamed to H2.
>

There are a lot of missing details. Here are some basic questions:
How was the pdb file generated ?
Are you sure this isn't an annoying feature of hydrogen naming,
ie, some of the usual issues with pdb files and hydrogens ?
What happens when pbsa is used instead of delphi ?

We gratefully accept detailed bug reports that contain short input
files for reproducible bugs. In fact those are our favorite ones :)
How to Report Bugs Effectively:
http://www.chiark.greenend.org.uk/~sgtatham/bugs.html

Scott

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