Hi Jason,
Thanks for your reply. I am using AmberTools 12 with updated patches . Is
there any ad hoc solution?
On Tue, May 14, 2013 at 5:34 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
*******************************************************************************************************************
Kshatresh Dutta Dubey, PhD
Post Doctoral Fellow
Indian Institute of Technology Kanpur
Kanpur, India
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 14 2013 - 06:00:02 PDT
