Hi Jason,
thanks for your help with my ligand setting problem.
I got it, and I really did not realize that I strip the water out :o)
Here's one thing I find strange with the MMPBSA.py script:
When starting pure PB calculations using
&pb
sander_apbs=1, indi=1,
/
I get the start of the output
ptraj found! Using /usr/local/amber11/bin/ptraj
sander found! Using /usr/local/amber11/bin/sander
sander.APBS found! Using /usr/local/amber11/bin/sander.APBS for PB
calculations
Warning: igb=5 should be used with either mbondi2 or bondi pbradii set.
Yours are modified Bondi radii (mbondi)
Preparing trajectories with ptraj...
and so on
with the Warning relating to GB calculations.
As gbsa is set to 1 by default, I tried to switch that of by adding a
section
&gb
gbsa=0
/
and to my surprise, the script starts doing GB calculation !?
I hope that you can reproduce that issue.
Best regards,
Oliver
--
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Thu Apr 21 2011 - 09:30:03 PDT
