Re: [AMBER] differences in PBSA energies (INP=1 verses INP=2)

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Sat, 15 Feb 2014 10:47:48 -0800

Divi,

If you're using AmberTools 13 with the latest patches applied, please
just use the default options for PB, i.e. only set inp=1 or inp=2 and
that should do it.

Our testing shows that inp=2 leads to less negative delta G's, and the
delta delta G's are smaller in magnitude (both are in better agreement
with experiment), but the smaller range of numbers also leads to lower
correlation. Let me know if you see a similar behavior.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Sat, Feb 15, 2014 at 9:29 AM, Divi/GMAIL <dvenkatlu.gmail.com> wrote:
>   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
>
>
>
>
>
>
>
>
>
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Received on Sat Feb 15 2014 - 11:00:07 PST