The complex internal energy terms are:
GENERALIZED BORN:
WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1046.0599 25.0584
3.5438
ANGLE 2825.6096 27.8852
3.9436
DIHED 3867.0393 20.6518
2.9206
VDWAALS -2766.8957 18.9666
2.6823
EEL -22450.1018 52.8100
7.4685
1-4 VDW 1296.0772 16.0482
2.2696
1-4 EEL 14608.9084 34.7009
4.9074
EGB -4636.7135 33.1652
4.6903
ESURF 146.7058 1.1452
0.1620
G gas -1573.3031 55.6723
7.8733
G solv -4490.0077 33.3028
4.7097
TOTAL -6063.3108 43.9275
6.2123
Similar for the Poisson-Boltzmann part. There is an image in that
email too. Not sure you got that picture ...
Ray
On Thu, Sep 19, 2013 at 11:16 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Thu, Sep 19, 2013 at 12:14 PM, Ray Luo, Ph.D. <ray.luo.uci.edu> wrote:
>
>> Your gas phase energies are huge and are consistent with the
>> screwed-up ligand figure attached in your email. The snapshots were
>> generated incorrectly somehow.
>
>
> That's not what I'm seeing:
>
> BOND = 25.8469 ANGLE = 65.0572 DIHED =
> 56.7073
> VDWAALS = -18.2347 EEL = 0.0000 EPB =
> -nan
> 1-4 VDW = 23.7188 1-4 EEL = 0.0000 RESTRAINT =
> 0.0000
> ECAVITY = 98.7361 EDISPER = 0.0000
>
> That was from the first snapshot of the attached _MMPBSA_ligand_pb.mdout
> file. The attached figure would result in gas phase energies _way_ higher
> than on the order of 10 kcal/mol... Something is killing the PB polar
> solvation calculation, but I'm not sure what. Am I missing something?
>
> All the best,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER.ambermd.org
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Received on Thu Sep 19 2013 - 12:00:03 PDT
