Changing the radii affects both PB and GB. You will be ok if you change
them now and use the new prmtop for mmpbsa.
On Apr 16, 2016 11:20 PM, "Jag Silwal" <jagsilwal.gmail.com> wrote:
> Dr. Carlos,
>
>
> Thank you for your prompt reply. With the little knowledge I have I didn't
> know that the radii were not used for any of the calculations during MD. As
> you have suggested, if I just recreate new files in Xleap with new radii
> and use those along with coordinate file from production step I would be ok
> then, right? For e.g. I would like to use a script similar to the one in
> tutorial with command line:
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp ras.prmtop -lp raf.prmtop -y
> *.mdcrd
>
>
> I just thought that the .mdcrd files from the production step is related to
> the radii set during the Xleap step and that would matter if I wanted to
> change the radii later after the simulation. But obvious lyI was wrong.
> Does changing the radii affect PBSA results or is it just the GB? Just
> curious.
>
>
> I will just recreate initial top and crd files in XLeap and I will rerun
> GB and PB accordingly.
>
>
> Again thank you for your valuable time,
>
>
> Jag
>
>
>
> On Sat, Apr 16, 2016 at 11:33 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > If your only use of gb is for post-processing, you can just generate a
> new
> > prmtop with the radii you want and use that for post-processing. You
> would
> > only consider rerunning if the radii were used during md. If you did
> > standard md in explicit solvent the radii were not used so do not matter
> > for the md part.
> > On Apr 16, 2016 10:30 PM, "Jag Silwal" <jagsilwal.gmail.com> wrote:
> >
> > > Dear all,
> > >
> > > I used "PBRadii mbondi 2" while generating topology and coordinate
> files
> > in
> > > X-leap. I need to run MMPB/GBSA analysis after simulations. Based on
> the
> > > amber manual igb =8 is the best for proteins but now I can't use igb=8
> > for
> > > GBSA because manual says that we have to use igb=2 or 5 for PBRadii
> > > mbondi=2 setup.
> > >
> > > I already ran MMPB/GBSA analysis with igb=5 but I was wondering if:
> > >
> > > a) There is a way to simply change the PBRadii mbondi to 3 without
> having
> > > to rerun the whole simulation again?
> > >
> > > b) I already ran PB/GB and alanine mutagenesis calculation using
> igb=5. I
> > > am guessing I need to rerun the calculation once the PBRadii is
> changed.
> > > right?
> > >
> > > Any helpful suggestions would be appreciated,
> > >
> > > Jag,
> > > _______________________________________________
> > > 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
> >
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Received on Sun Apr 17 2016 - 05:00:04 PDT
