AMBER Archive (2006)

Subject: AMBER: sander/topology problem

From: Lorenzo Gontrani (l.gontrani_at_caspur.it)
Date: Tue Oct 17 2006 - 11:51:39 CDT

Dear Amber users, I am experiencing a problem I had never encountered before..
I built my system topology with LeaP, adding solvent molecules as usual. I
then minimized the system (SD, then conjugate gradient). I checked the
results by writing PDB files, and all was OK. Then I turned to box pressure
equilibration, running a simulation at low temperature with tight coupling
(taup = 0.01).
At the end of the run, i visualized the resulting PDB files and the ligand had
three C-H bond broken, H atoms had flown apart.
What can have happened? I cannot explain it..
Thanks for any help

Lorenzo 

-- 
=======================================

Lorenzo Gontrani

CASPUR - http://www.caspur.it
Consorzio per le Applicazioni di Supercalcolo Per Università e Ricerca
via dei Tizii, 6 - 00185 Roma
Tel +39 06 44486812 
Fax +39 06 4957083 
GSM +39 338 7615798
Email l DOT gontrani AT caspur DOT it

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