Re: AMBER: Antechamber problem

From: David A. Case <>
Date: Tue, 23 Sep 2003 08:19:54 -0700

On Mon, Sep 22, 2003, Shafinaz wrote:

> I've been using Amber for about a year now to run MD simulations on
> a series of small molecules in waterboxes. I was using an older version of
> Amber 7 (older in the sense that it was compiled in 2001), and antechamber
> was working fine. For example, a prepin file created for methane using amber
> atom types assigned the hydrogens the HC type, and the carbon the CT type.
> We recently recompiled Amber 7 (July of this year), and now the ante-
> chamber program assigns erroneous atom types, especially in the case of
> hydrogen atoms. For example, the exact same procedure for methane (same mol2
> file, same antechamber options) creates a prepin file with hydrogens
> assigned
> HA atom types. Can anyone explain why this is happening? Thanks,

You don't make it clear what has changed: the code? the machine you are
compiling it on? In either case, what do you think the key differences are?
Does the new code pass or fail the test suite?


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:                   
La Jolla CA 92037  USA            |
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Received on Tue Sep 23 2003 - 16:53:00 PDT
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