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--- This will create a topology file "new_radii.prmtop" with the mbondi3 radii instead of whatever you had before. It recognizes the same keywords that tleap does. HTH, Jason On Sun, Apr 17, 2016 at 7:53 AM, Carlos Simmerling < carlos.simmerling.gmail.com> wrote: > 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 > > > > > _______________________________________________ > > 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 > -- Jason M. Swails _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Apr 17 2016 - 08:30:03 PDT