AMBER Archive (2005)

Subject: AMBER: mm_pbsa script !

From: Pradipta Bandyopadhyay (pradipta_at_iitg.ernet.in)
Date: Mon Jun 27 2005 - 01:43:53 CDT

I have a doubt if make_crd_hg.f used during the MMPBSA snapshot generation
has a minor bug or not.

 Line 532 of make_crd_hg.f says if NGREC .gt. 0 (# of receptor groups) and
RSTART(j) .lt. LSTART(k) (the number of starting atom of receptor is less
than that of ligand) OR k. gt. # of ligand groups, then look for
receptor atoms.

However, since in line 86, RSTART(1) ----- RSTAR(10) are initialized to 0.
Even if I define only one receptor group. According to line 532, it finds
RSTART(2) .LT. LSTART(k) and looks for receptor atoms and the code crashes.

If we put another option in line 532 that RSTART(j) has to be more than 0,
then it works fine.

Am I doing it correctly? I would appreciate any help.

                     Pradipta

Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati
Phone: 91-361-258-2213 (office)
e-mail: pradipta_at_iitg.ernet.in
web: http://202.141.80.5/~pradipta/Pradipta.htm

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