Hello all,
I have been doing research modeling inhibitors of enzymes and have recently run into a problem in which the ligand immediately breaks apart once the simulation starts. When I have visualized the simulation it appears as though the atoms in the ligand move independently but somehow maintain bonds even if they are over 10 angstroms apart. This seems to be a more recent issue that I did not have while doing this research in the past. I have been using periodic boundaries and heating using NVT, then equilibrating with NPT. The one thing that I have found that works is if I turn off periodic boundaries, however I would like to be able to keep the system at constant pressure. I have not seen any previous posts of this problem happening and am wondering if anyone has some suggestions.
Thanks,
Luke Presson
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 01 2016 - 06:30:06 PDT
