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.
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Received on Wed May 02 2012 - 06:00:05 PDT
