If this is AmberTools 13, there is an issue with the inp=1 nonpolar
solvation term. A fix is in the works, but not available yet. We hope to
have it soon.
All the best,
Jason
On Tue, May 14, 2013 at 6:34 AM, Kshatresh Dutta Dubey
<kshatresh.gmail.com>wrote:
> Dear Users,
>
> I am calculating binding free energy for protein-peptide complex. When I am
> using inp=1 and radiopt=0, I am getting a large difference between delta G
> for GB and PB calculations. While, if I am using inp=2, radiopt=0 (
> http://archive.ambermd.org/201208/0089.html), I am getting PB bomb error
> during MMPBSA.py run. Following are my input and corresponding outputs for
> MMPBSA calculations-
>
> *Input file for running PB and GB*
> &general
> startframe=1000, endframe=1400, interval=50,verbose=2,
> entropy=1, strip_mask=:WAT:Na+,
> /
> &gb
> igb=5, saltcon=0.150,
> /
> &pb
> istrng=0.100,fillratio=4.0,
> inp=1, radiopt=0,
> /
>
> *Corresponding output is- *
> For GB section-
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 0.0000 0.0000
> 0.0000
> ANGLE 0.0000 0.0001
> 0.0000
> DIHED -0.0000 0.0000
> 0.0000
> VDWAALS -110.1017 7.0312
> 1.5343
> EEL -225.7126 19.0563
> 4.1584
> 1-4 VDW 0.0000 0.0001
> 0.0000
> 1-4 EEL 0.0000 0.0000
> 0.0000
> EGB 295.7762 17.6341
> 3.8481
> ESURF -14.2568 0.7890
> 0.1722
>
> DELTA G gas -335.8143 21.0157
> 4.5860
> DELTA G solv 281.5194 17.3843
> 3.7936
>
> *DELTA TOTAL -54.2949 7.9276
> 1.7299*
>
>
> and for PB section-
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
>
> -------------------------------------------------------------------------------
> BOND 0.0000 0.0000
> 0.0000
> ANGLE 0.0000 0.0001
> 0.0000
> DIHED -0.0000 0.0000
> 0.0000
> VDWAALS -110.1017 7.0312
> 1.5343
> EEL -225.7126 19.0563
> 4.1584
> 1-4 VDW 0.0000 0.0001
> 0.0000
> 1-4 EEL 0.0000 0.0000
> 0.0000
> EPB 273.6640 17.4261
> 3.8027
> ENPOLAR 2342.0140 114.0742
> 24.8930
> EDISPER 0.0000 0.0000
> 0.0000
>
> DELTA G gas -335.8143 21.0157
> 4.5860
> DELTA G solv 2615.6780 120.3178
> 26.2555
>
> *DELTA TOTAL 2279.8638 108.7266
> 23.7261
> *
>
> Results of PB and GB section have very large difference. I will deeply
> appreciate if someone help me to figure out this problem.
> --
> With best regards
>
> *******************************************************************************************************************
> Kshatresh Dutta Dubey
> Post Doctoral Fellow
> Indian Institute of Technology Kanpur
> Kanpur, India
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 14 2013 - 05:30:03 PDT
