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
>>
>
>
>
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Received on Tue May 14 2013 - 06:00:02 PDT
