AMBER Archive (2005)

Subject: Re: AMBER: Mg2+ issues of using MM-PB/GBSA

From: Ray Luo (rluo_at_uci.edu)
Date: Wed Nov 30 2005 - 22:31:29 CST


The radii are assigned in routine "pb_aaradi()" in file "pb_init.f". You
can add a line there to assign radius for the ion and recompile. You can
set npbverb=1 to print out more information in the output file to check
your radii assignment.

mingche Pan wrote:

> Thank you, Ray! I guess that is the reason why all PB energies are the
> same. I will rerun the PB calculations. So when I used radiopt =1,
> where thoes parameters come from?
>

-- 
====================================================
Ray Luo, Ph.D.
Department of Molecular Biology and Biochemistry
University of California, Irvine, CA 92697-3900
Office: (949)824-9528         Lab: (949)824-9562
Fax: (949)824-8551          e-mail: rluo_at_uci.edu
Home page: http://rayl0.bio.uci.edu/rayl/
====================================================

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu