AMBER Archive (2005)

Subject: AMBER: strange mm_pbsa.pl bug

From: Nelson Fonseca (nfonseca_at_dq.ua.pt)
Date: Mon May 16 2005 - 10:39:21 CDT


Experience is what you get when you don't get what you
want.

                      -- Dan Stanford--

Dear all,

Im having a strange problem that I cannot understand in
mm_pbsa calculations. The total charge of my molecule is
+6.
When I look carefully all the output files that are
generated during the execution of the script, I have
noticed that the total charge from the sander_rec.out is
correct (+6) but when I look at the correpondent
sanmin_rec.out the total charge of my molecule is +3!! Im
using exactly the same topology file for the run!

Could it be a bug? It sounds to me very strange........

thanks in advance for your help

Nelson Fonseca
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