Re: [AMBER] Using with CHARMM force field

From: Jason Swails <>
Date: Fri, 21 Aug 2015 09:40:41 -0400

On Thu, Aug 20, 2015 at 4:43 PM, Ara Abramyan <> wrote:

> Dear Amber users,
> I want to do mmpb(gb)sa calculations for a protein/ligand "dry" complex
> using 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 -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:
> -rp -lp -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 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.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Aug 21 2015 - 07:00:05 PDT
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