[AMBER] Using MMPBSA.py with CHARMM force field

From: Ara Abramyan <araabramyan.gmail.com>
Date: Thu, 20 Aug 2015 16:43:11 -0400

Dear Amber users,

I want to do mmpb(gb)sa calculations for a protein/ligand "dry" complex
using MMPBSA.py package with CHARMM c36 topology/parameter and coordinate
files. I do not get any errors but I just want to know what is the
"optimal" method for this type of calculations.

My steps are:

I convert the CHARMM files into AMBER topology and coordinate files.Here is
an example of my script for the complex

$AMBERHOME/bin/chamber -cmap -top top_all36_prot.rtf -param
par_all36_prot.prm -str myligandfile.str -psf mypsffile.psf -crd
mypdbfile.pdb -p ambertopfile.top -inpcrd ambercrdfile.crd

For the complex and protein I use -cmap for ligand I use -nocmap. For
protein I do not use the -str flag.

Next I use cpptraj to convert my pdb coordinates into amber .crd format

Finally I do the mmpbsa run like this:

$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
ambertopfile.top -rp amberrectopfile.top -lp amberligtopfile.top -y *.crd
-eo frames.out


-I get positive numbers from the PB results... The PB part fails if I use
radiopt=1 and works only with radiopt=0, is this the right way to do or I
should use different radii?

-For GB part, which igb method shall I use? I tried the igb=2 and igb=5
(the mbondi is the default 2 from chamber), which one is considered to be
the most "accurate"?

-and generally when converting files from CHARMM and calculating energies
with MMPBSA.py package, are there any exceptions from the default values to
run the calculations?


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Received on Thu Aug 20 2015 - 14:00:03 PDT
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