Hello all:
I am doing free-energy analysis of some mutants in a protein system with
three domains (1-372; 373-713; 714-1356 residues). For some reason, the new
methodology of PBSA (inp=2) compared to inp=1 is giving Delta-G numbers I am
not very comfortable.
Can someone check the following two inputs and the corresponding energies
I have for a WT structure? The numbers between GB and PB are "comparable"
with INPUT-1 rather than INPUT-2.
Am I missing some important keyword/variable in the input or making some
mistake in calculations? I greatly appreciate your comments/suggestions.
--- I am using fully patched version
AmberTools version 13.22
Amber version 12.21
-- All the MD stuff done on GPU-TITAN and free-energy analysis on
60-processors using MMPBSA.py.MPI (on our local DELL cluster)
_________________________________________________________________________
INPUT-1
&general
debug_printlevel=0, verbose=2, keep_files=1, netcdf=1,
startframe=11, endframe=550, interval=9,
ligand_mask=":373-713", receptor_mask=":1-372:714-1356",
strip_mask=:WAT,COP,CAL,Cl-,
use_sander=1, entropy=0,
/
&gb
igb=8, surften=0.005, surfoff=0.0, saltcon=0.100,
/
&pb
inp=1, radiopt=0,
cavity_offset=0.9200, cavity_surften=0.00542,
istrng=0.100,
/
INPUT-2
&general
debug_printlevel=0, verbose=2, keep_files=1, netcdf=1,
startframe=11, endframe=550, interval=9,
ligand_mask=":373-713", receptor_mask=":1-372:714-1356",
strip_mask=:WAT,COP,CAL,Cl-,
use_sander=1, entropy=0,
/
&gb
igb=8, surften=0.005, surfoff=0.0, saltcon=0.100,
/
&pb
inp=2, radiopt=1,
cavity_offset=-0.5692, cavity_surften=0.0378,
indi=1.0, exdi=80.0, scale=2.0,
linit=1000, fillratio=4, prbrad=1.4,
istrng=0.100,
/
INPUT-1 (PBSA)
DELTA G gas -1724.7566 80.9085
10.4452
DELTA G solv 1579.8692 74.4081
9.6061
DELTA TOTAL -144.8874 15.9947
2.0649
INPUT-2 (PBSA)
DELTA G gas -1724.7566 80.9085
10.4452
DELTA G solv 1829.9470 80.4638
10.3878
DELTA TOTAL 105.1904 20.1341
2.5993
INPUT-1 (GBSA)
DELTA G gas -1724.7566 80.9085
10.4452
DELTA G solv 1608.9945 74.0431
9.5589
DELTA TOTAL -115.7621 11.3484
1.4651
INPUT-2 (GBSA)
DELTA G gas -1724.7566 80.9085
10.4452
DELTA G solv 1608.9945 74.0431
9.5589
DELTA TOTAL -115.7621 11.3484
1.4651
___________DATA_END__________________________________
Thanks and regards
Divi
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Feb 15 2014 - 09:30:03 PST
