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,
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Sat Apr 16 2016 - 21:30:03 PDT
