Hi Jan-Philip,
Thanks for help. I will go through this and can also wait for amber
official update, if this does not work.
On Tue, May 14, 2013 at 6:09 PM, Jan-Philip Gehrcke <jgehrcke.googlemail.com
> wrote:
> Kshatresh,
>
> if you want to take the risk and not wait for an official update, then
> this is the patch Qin proposed. It seems to work for me:
>
> --- a/AmberTools/src/pbsa/pb_read.F90
> +++ b/AmberTools/src/pbsa/pb_read.F90
> .. -1043,9 +1043,9 .. subroutine pb_read
> & and should not be used with inp=1. It has been reset to
> -1.008.'
> cavity_offset = -1.008d0
> end if
> -! if ( radiopt == 0 ) then
> -! donpsa = .false.
> -! end if
> + if ( inp == 1 ) then
> + donpsa = .false.
> + end if
>
> ! check force options
>
> Apply it, recompile PBSA and see what happens. Note that you might
> undermine Amber's automatic update system with this irregular patch.
>
> Cheers,
>
> Jan-Philip
>
>
>
>
> On 05/14/2013 02:32 PM, Kshatresh Dutta Dubey wrote:
> > 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
> >>
> >
> >
> >
>
>
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With best regards
*******************************************************************************************************************
Kshatresh Dutta Dubey, PhD
Post Doctoral Fellow
Indian Institute of Technology Kanpur
Kanpur, India
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Received on Tue May 14 2013 - 06:00:03 PDT
