AMBER Archive (2006)

Subject: AMBER: Q: results from PB solver in example no.3

Date: Wed Jan 04 2006 - 17:09:42 CST

Dear All,

I am currently working under the directory, "amber8/src/mm_pbsa/Examples/03_MMPBSA_binding. I am trying to perform benchmark of ZAP (from Openeye) as an additional PB solver. However, I am stuck in a situation where I can not be sure whether the introduction of ZAP is proper or not, because ZAP gave a different answer. So please give me your suggestion and comment for the following questions and requests.

Q1) The final result stored in "ras_raf_II_wt_statistics.out", I found that values of PBTOT (-66.2) and GBTOT (-51.4) are quite different. Is the difference between the two methods common? Are they should be closer in theory?

Q2) If one or another is better, which value we should take? PBTOT or GBTOT?

Q3) When I introduced ZAP, I got -96.1 for PBTOT which is far different from the above two values. What do you think?

Request ) Did anyone calculate PBTOT by using Delphi starting from the same input file in the directory? If you did not yet and have Delphi in your hand, could you possibly calculate it? The value of PBTOT (-66.2) in the directory was given from AMBER's PB solver. I want to know what value a world standard software gave?

Thank you in advance.

Masaki Tomimoto
Takeda Pharmaceutical
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