I would avoid using GB models for this type of work. They are intended for
situations where the calculation must be fast, not for postprocessing a
limited number of frames.
GB has additional parameters that are typically not optimized for the range
of chemistry seen in the complexes that people use with MMPBSA.
beyond that, keep in mind that MMPBSA is approximate at best, and you
should run the analysis on independent simulations to obtain precision
estimates.
On Thu, Apr 11, 2024 at 3:22 PM Kaleem Arshad via AMBER <amber.ambermd.org>
wrote:
> Hi, respected AMBER users, I ran 50ns simulation of levonadifloxacin with
> one of mycobacterial protein. The MM-GBSA predicted binding energy is about
> -41kcal/mol while that by MM-PBSA is +11kcal/mol. I am unable to figure it
> out completely as in AMBER tutorial there is no mention of ENPOLAR and
> EDISPER energy terms rather only ECAVITY is mentioned alongwith EPB. I used
> following input to run calculation:
> MM-PBSA Calculation
> &general
> startframe=1, interval=10,
> verbose=2, keep_files=2, netcdf=1,
> /
> &pb
> istrng=0.15, fillratio=4.0,
> /
> what should be the best practice with such kind of results?
> Thanking you in advance
> I am sorry in advance if my question appears ambiguous.
> Regards,
> Kaleem
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 11 2024 - 13:00:02 PDT
