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.eml-r.villa-bosch.de
Web: http://www.embl-heidelberg.de/~twang
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Mon Jun 21 2004 - 14:53:00 PDT
