AMBER Archive (2003)

Subject: AMBER: Antechamber problem

From: Shafinaz (shafinaz_at_bri.nrc.ca)
Date: Mon Sep 22 2003 - 11:33:58 CDT

Hello,
        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,

Shafinaz F. Chowdhury, PhD
Research Associate,
Computational Chemistry,
Biotechnology Research Institute,
National Research Council of Canada.
Email: shafinaz_at_bri.nrc.ca
Tel: 514 496 6338
Fax: 514 496 5174

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