100 snapshots from last 1ns of stable simulation results very different
binding energies from PB and Gb models, which is also doubtful to me. I
would try last 4-5 nd with at least 200 snapshots and see how does it
affects the result.
On Tue, Feb 14, 2012 at 11:04 AM, Urszula Uciechowska <
urszula.uciechowska.chem.umu.se> wrote:
> I took 100 sps, from the las 1ns of my MD simulation.
> I have checked the RMSD and energies and based on that system was stable,
> thus I decided to run MMPBSA.
>
> /Urszula
>
> ________________________________________
> Von: mish [smncbr.gmail.com]
> Gesendet: Dienstag, 14. Februar 2012 10:26
> An: AMBER Mailing List
> Betreff: Re: [AMBER] MMPBSA results and huge SD
>
> What do you mean by "I run MMPBSA calculations for a protein-peptide
> complex for 100 sps" ? What I can think of is ..you take snapshots at each
> 100ps from a 10ns long MD simulation of the complex. Best would be to
> choose the last few ns of your MD simulation where your system had stable
> dynamics. Have a look in the backbone RMSD of protein and also in the
> energies so that you can decide what part of your MD simulation is not
> stable and need to be excluded from the calculations.
>
> Hope it helps.
>
> Sincerely
> Mish
>
>
> On Tue, Feb 14, 2012 at 10:14 AM, Urszula Uciechowska <
> urszula.uciechowska.chem.umu.se> wrote:
>
> >
> > Dear Amber users,
> >
> > I run MMPBSA calculations for a protein-peptide complex for 100 sps. The
> > MD simulations were carried out for 10ns, complex was stable...
> > below I pasted the results that I received from mmpbsa run, what I dont
> > understand is this huge STD value ... ? why is that? where does it come
> > from?
> > I have also checked the single sps and rerun MMPBSA, however I have not
> > seen such as big deviation.
> > How should I understand PBTOT= -129.74 with STD=75.51?
> >
> >
> >
> > # DELTA
> > # -----------------------
> > # MEAN STD
> > # =======================
> > ELE -322.09 138.62
> > VDW -86.14 39.01
> > INT 0.00 71.77
> > GAS -408.23 152.07
> > PBSUR -80.64 9.24
> > PBCAL 359.13 122.81
> > PBSOL 278.49 119.83
> > PBELE 37.04 50.97
> > PBTOT -129.74 75.51
> > GBSUR -13.50 1.53
> > GB 447.06 132.54
> > GBSOL 433.56 132.07
> > GBELE 124.97 86.27
> > GBTOT 25.33 109.88
> >
> >
> > Thank you in advance for any comments,
> >
> > best regards
> > Urszula
> > _______________________________________________
> > 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
>
> _______________________________________________
> 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 Tue Feb 14 2012 - 03:00:02 PST
