Dear Ray,
I repeat my problem again in detail. I am a user of Amber11 and use Amber tools11. Try to calculate electrostatic potential surface using PBSA and hence follow section 7.3.2 of Amber tools11. I use the following comman-
pbsa –O –i mdin –o mdout –p prmtop –c inpcrd
The problem is that the pbsa.phi (renamed as 1VJ5pbsa.phi) file generated is not loaded in PyMol. But using the same mdin, prmtop and inpcrd file Qin generate a pbsa.phi file in Amber11 and this pbsa.phi is successfully loaded in PyMol. Qin suggested that the two pbsa.phi files are apparently different, but the difference between them is not clear. I analyzed two mdout file (generated by me and Qin) and found some difference between them. Some portion of these differences is given below-
Qin mdout-
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box at level: 2
Bounding Box Center: 7.000 65.000 114.000
Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553
Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245
Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810
beginning box center at level 2 7.000 65.000 114.000
Grid dimension at level 2 41 41 41
Grid origin corrected at level 2 -14.000 44.000 93.000
Bounding Box at level: 1
Bounding Box Center: 7.000 65.000 114.000
Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553
Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245
Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810
beginning box center at level 1 7.000 65.000 114.000
Grid dimension at level 1 7 7 7
Grid origin corrected at level 1 -25.000 33.000 82.000
------- VMD goodie --------
#First Level Geometric Box
draw materials off
draw color green
draw line " -25.000 33.000 82.000" " 31.000 33.000 82.000"
My mdout-
======== Setting up Grid Parameters ========
Using bounding box for grid setup
Bounding Box Center: 7.000 65.000 114.000
Xmin, Xmax, Xmax-Xmin: -3.759 17.794 21.553
Ymin, Ymax, Ymax-Ymin: 55.004 74.249 19.245
Zmin, Zmax, Zmax-Zmin: 106.134 120.944 14.810
beginning box center at level 1 7.000 65.000 114.000
beginning box center at level 2 7.000 65.000 114.000
Grid dimension at level 1 7 7 7
Grid origin corrected at level 1 -25.000 33.000 82.000
Grid dimension at level 2 41 41 41
Grid origin corrected at level 2 -14.000 44.000 93.000
Many parameters is absent in my mdout file. While Qin and I both use the same mdin, prmtop, inpcrd and same version of amber, why this difference arises? What is the problem associated with my pbsa.phi (1VJ5pbsa.phi). Qin said to forward this problem to Wes. I attached two mdout (1VJ5mdout for my calculation and mdout for Qin calculation), prmtop, inpcrd, mdin and two pbsa.phi file with this mail. I think I express my problem properly. Please let me know about this problem. I am looking for your answer.
With Best Regards,
Sudarshan.
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- text/plain attachment: mdout
- application/octet-stream attachment: pbsa.phi
- text/plain attachment: mdin
Received on Wed May 16 2012 - 03:00:02 PDT
