Okay, At least we know it is working somehow ... I remember Qin said
he used your input file ... but I'll let Qin to confirm which input
file he used ...
Ray
---------- Forwarded message ----------
From: Sudarshan Debnath <sudarshandebnath.ku.rediffmail.com>
Date: Wed, May 2, 2012 at 5:54 AM
Subject: [AMBER] Electrostatic potential calculation
To: amber.ambermd.org
Dear Ray & Qin,
Many many thanks. I think this problem is not
associated with PyMol but with the procedure by which I calculate esp
surface in Amber11 (not sure but a guess). Qin generated the pbsa.phi
using 1VJ5.rst and 1VJ5.top file that I attached with mail. I loaded
the pbsa.phi created by Qin and mapped the potential surface (I
attached an image file with this mail). Where as the 1VJ5pbsa.phi that
I generated from the same 1VJ5.rst and 1VJ5.top file are not loaded in
PyMol. So, I think there is problem in 1VJ5pbsa.in file or command
used for pbsa calculation. I attached the 1VJ5pbsa.in and 1VJ5pbsa.out
file, please check it. Can I get the input, output file and details of
the procedure (command) that used by Qin, please. By the way I use the
following command-
./pbsa -O -i 1VJ5pbsa.in -o 1VJ5pbsa.out -p 1VJ5.top -c 1VJ5.rst
I am looking for your answer.
With the best regards,
Sudarshan.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 02 2012 - 10:30:04 PDT
