On Thu, Aug 20, 2015 at 4:43 PM, Ara Abramyan <araabramyan.gmail.com> wrote:
> 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
>
> Questions:
>
> -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?
>
radiopt=0 is the only way to go here. The atom types for the optimized
radii in PB has only been set for the Amber force field atom types (and
even then, not *all* of the Amber force fields...)
I would also suggest switching to inp=1, which usually behaves quite a bit
better when inp=2 gives rather absurd answers.
> -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"?
>
There isn't a huge difference between them, but papers I recall reading
tagged igb=5 as the preferred model, I think.
> -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?
>
MM/GBSA energies, you usually don't have to change the default parameters.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 21 2015 - 07:00:05 PDT
