Hi all,
I am having some troubles with the module sander.
If I use sander of AT14 for executing a minimisation,
I obtain the following "nice" energy breakdown:
BOND = 30.4484 ANGLE = 188.7898 DIHED = 113.9438
VDWAALS = ************* EEL = 409.0441 EGB = 0.0000
1-4 VDW = 53.2129 1-4 EEL = -1105.5194 RESTRAINT = 0.0000
where the high VDW energy is simply due to some atom clashes.
Whereas if I feed sander of either Amber11 or Amber12 with
exactly the same topology and coordinates files I obtain different values only
for the 1-4 VDW and EEL energies (which are *Not a Number* and
*-Inf* respectively):
BOND = 30.4484 ANGLE = 188.7898 DIHED = 113.9438
VDWAALS = ************* EEL = 409.0441 EGB = 0.0000
1-4 VDW = NaN 1-4 EEL = -Infinity RESTRAINT = 0.0000
Since my molecule is a modified residue, hence
I would like to make sure that I'm
correctly treating the system.
Does anybody have any explanation for this behaviour?
If necessary, I can send my files off list.
Thanks in advance,
--
Dr Massimiliano Porrini
Valérie Gabelica Team
U869 ARNA - Inserm / Bordeaux University
Institut Européen de Chimie et Biologie (IECB)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 63 31
http://www.iecb.u-bordeaux.fr/teams/GABELICA
Emails: m.porrini.iecb.u-bordeaux.fr
mozz76.gmail.com
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Received on Thu Jul 10 2014 - 11:30:02 PDT
