On Fri, Jul 4, 2014 at 2:10 AM, Sourav Purohit <sour000.gmail.com> wrote:
> While setting up simulation for a complex, I did not set default PBRadii to
> mbondi2. Now I plan to perform MMPBSA calculation for the complex. Will I
> get wrong results if i use igb=2 ?
>
You should set your radii to the recommended set for the GB value. Energy
differences with GB can be quite sensitive to small changes in intrinsic
radii (this sensitivity is especially enhanced when the net charge changes,
like with pKa calculations).
You can use ParmEd to change the solvent radii without having to go through
tleap again. Something like this:
parmed.py -p <your.prmtop> << EOF
changeRadii mbondi2
parmout new.prmtop
EOF
Alternatively, you can use xparmed.py if you prefer a GUI that you can
click with. In this case, just running "xparmed.py" will bring up a file
browser, or "xparmed.py <file>" will bring up the action window where you
can modify your topology file. More information here:
http://jswails.wikidot.com/parmed
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 04 2014 - 12:30:02 PDT
