This could be due to a mismatch between the topology files that you
provided and the trajectories created by MMPBSA.py from your original
trajectory. You should try visualizing the trajectories made by MMPBSA.py
with their corresponding topology files that you provided to see if they
look right. If they do not, it is likely because there is some mismatch
between the residues in the topology files, possibly ions or other residues
that were unintentionally removed? You can also check the mdout files
created by MMPBSA.py to see if they provide any helpful messages.
-Bill
On Wed, Apr 3, 2013 at 9:50 AM, Albert <mailmd2011.gmail.com> wrote:
> Thanks for kind reply.
>
> It seems to work, but the results are quite strange, I don't understand
> why the DELTA TOTAL is -nan...............
>
>
>
> Complex:
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -nan nan nan
> EEL inf nan nan
> EPB -3814.2285 167.4644 74.8924
> ENPOLAR -13229.5291 267.2825 119.5324
>
> G gas -nan nan nan
> G solv -17043.7576 365.7608 163.5732
>
> TOTAL -nan nan nan
>
>
> Receptor:
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -nan nan nan
> EEL inf nan nan
> EPB -3863.0509 173.6680 77.6667
> ENPOLAR -13373.3513 259.4847 116.0451
>
> G gas -nan nan nan
> G solv -17236.4022 338.9629 151.5888
>
> TOTAL -nan nan nan
>
>
> Ligand:
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> VDWAALS 0.3505 0.8443 0.3776
> EEL -23.6928 0.5955 0.2663
> EPB -13.5896 0.3189 0.1426
> ENPOLAR -361.8551 3.6889 1.6497
>
> G gas -23.3423 0.7728 0.3456
> G solv -375.4447 3.8267 1.7113
>
> TOTAL -398.7869 3.7756 1.6885
>
>
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err.
> of Mean
>
> -------------------------------------------------------------------------------
> VDWAALS -nan nan nan
> EEL -nan nan nan
> EPB 62.4120 34.7810 15.5545
> ENPOLAR 505.6772 18.2805 8.1753
> EDISPER 0.0000 0.0000 0.0000
>
> DELTA G gas -nan nan nan
> DELTA G solv 568.0892 43.8595 19.6146
>
> DELTA TOTAL -nan nan nan
>
>
>
> -------------------------------------------------------------------------------
>
>
>
>
>
>
>
>
>
>
> On 04/03/2013 01:53 PM, Jason Swails wrote:
> > Just a clarification -- this should be "inp=1" and "radiopt=0", since
> inp=2
> > is the default that forces radiopt=1. The problem with radiopt=1 in this
> > case is that there are no optimized radii for one of your atom types.
> > Ergo, the easiest solution is to just take it from the prmtop (i.e.,
> > radiopt=0).
> >
> > Good luck,
> > Jason
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Wed Apr 03 2013 - 07:30:02 PDT
