AMBER Archive (2004)

Subject: AMBER: solvate proteins in xleap/amber8

From: Ting Wang (wang_at_eml-r.villa-bosch.de)
Date: Mon Jun 21 2004 - 08:20:03 CDT

Dear AMBER users,

I am not sure if this is a bug in amber8.
I was trying to solvate my protein in xleap: solvateOct mol TIP3PBOX
12.0, I got more than 10K water molecules, the density > 3 g/cc, and the
protein is not fully covered by water. But when I used amber7:
solvateOct mol WATBOX216 12.0, I got 4391 wat and a density of 0.870
g/cc and the protein is fully covered by wat.

The machine/OS details :

compilation: intel compilers on Intel(R) Xeon(TM) CPU 2.40GHz,Linux
version 2.4.24 (gcc version 2.95.4 20011002 (Debian prerelease))

Running: 1. the same machine as compilation.
          2. AMD Athlon(tm) Processor 1.4GHz.Linux version 2.4.20 (gcc
version 2.95.4 20011002 (Debian prerelease))

Best,

Ting 

--
Dr. Ting Wang

Molecular & Cellular Modelling
EML Research gGmbH

Villa Bosch
Schloss-Wolfsbrunnenweg 31c
69118 Heidelberg
Germany
Tel: +49 6221 533 262
Fax: +49 6221 533 298
Email: ting.wang_at_eml-r.villa-bosch.de
Web:   http://www.embl-heidelberg.de/~twang

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