Dear Ray and Qin,
I install Amber tools 12 as you suggested and calculate the electrostatic potential. I am very sorry to say the same problem is arises that is the pbsa.phi is not loaded in PyMol (PyMol stop working). In the VMD the pbsa_phi.dx is loaded but the isosurface representation is not acceptable (please see the image attached with mail). I also analyze again the two mdout file (created by Qin and me). Now there is no remarkable difference, the two mdout file is same. So something is different in pbsa.phi and pbsa_phi.dx file. I attached pbsa_phi.dx file in next mail. Please check it. Why this problem arises, is there any thing that I miss? Please let me know. I told that I successfully loaded the pbsa.phi in PyMol using Amber Tools 1.5, but it is a wrong result, because the esp gradient can not be appeared by this result. I am very sorry for that.
With best regards,
Sudarshan.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
- application/octet-stream attachment: 1VJ5.rst
- application/octet-stream attachment: 1VJ5.top
- application/octet-stream attachment: mdout
- application/octet-stream attachment: pbsa.phi
- application/vnd.openxmlformats-officedocument.wordprocessingml.document attachment: Doc1.docx
Received on Mon May 21 2012 - 12:30:04 PDT
