[AMBER] ESURF in MMPBSA.py results

From: Huang <huangloligo.gmail.com>
Date: Fri, 15 May 2015 16:26:22 +0800

I read the output files _MMPBSA_{complex,ligand,receptor}_gb.mdout.0
after an MMPBSA.py run with Input file:
|Poisson-Boltzmann and General Born
| debug_printlevel=1,
| verbose=2,
| startframe=10,
| endframe=10,
| use_sander=0,
| strip_mask=":WAT,NA,CL",
| entropy=0,
| keep_files=1,
| saltcon=0.100,

There is a ESURF value in each of these file, but this value is
different from the ESURF value in the finally output file (assigned by
option -o of MMPBSA.py). I read the reference manual and the source
code of MMPBSA.py and realize that MMPBSA.py calculates ESURF values
by invoking cpptraj with command surf (LCPO method) or molsurf
(Connolly's method).

The questions :
1. Why does MMPBSA.py discard the values of ESURF in
2. Neither LCPO nor Connolly's method, within cpptraj, produces values
comparable to the values in
_MMPBSA_{complex,ligand,receptor}_gb.mdout, i.e. the difference is
larger than acceptable error. What is the exact method used in these
files? Is it really ESURF in the context of free energy calculation?

I am looking forward to your reply.

Best regards,

AMBER mailing list
Received on Fri May 15 2015 - 01:30:04 PDT
Custom Search