AMBER Archive (2009)

Subject: RE: [AMBER] Radius for Bromine in MMPBSA calculation

From: Ray Luo (ray.luo_at_uci.edu)
Date: Tue May 26 2009 - 14:02:27 CDT

Well, I hate to say this ... we'll come up with a better solution in the
next release.

All the best,
Ray

==========================================
Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email: rluo_at_uci.edu
Phones: (949) 824-9528, 9562
Web: http://rayl0.bio.uci.edu/
==========================================

-----Original Message-----
From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On Behalf
Of john smith
Sent: Monday, May 25, 2009 10:01 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Radius for Bromine in MMPBSA calculation

Dr. Luo

Thanks a sdlot for your reply. I had searched the archive and came to
the conclusion that the solution which I had tried earlier was
correct. However there is a small problem.
I have two prmtop files for two different ligands( each containing
bromine). In prmtop for the ligand m12, bromine atom has been numbered
1 as Br1, and in another for the ligand m13, it has been numbered as
Br21.

If I add radius for Bromine as "Br" => 1.850, then calculation does
not runs to completion for any of the ligand.
If I add radius for Bromine as "Br1" => 1.850, then calculation
completes for ligand m12 only.
And if I add radius for Bromine as "Br21" => 1.850, then calculation
completes for ligand m13 only.

Hence can you please suggest me some possible solution, so that
calculation becomes independent of the atom number given to Bromine in
the prmtop file as in the case of othert elements.

Regards
-John

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber