Re: [AMBER] MMGBSA on Protein-DNA/RNA complex

From: Jason Swails <>
Date: Wed, 24 Jun 2015 08:27:32 -0400

On Wed, Jun 24, 2015 at 4:02 AM, Muthukumaran R <>

> I tried MMPBSA, with following input on amber tools 14 (AMBER12)
> Sample input file with pb analysis
> &general
> startframe=15000, endframe=20000,interval=50,
> verbose=2, keep_files=1,
> /
> &pb
> istrng=0.1, indi=4, scale=2, inp=2,
> /
> when I included the option "ipb=1" in &general or &pb, it gives the same
> error
> InputError: Unknown variable ipb in &pb.

​ makes no use of the ipb variable. It is automatically set to 1
in the sander or mmpbsa_py_energy input files. If you want to change this
value to something *besides* 1, you probably need to set use_sander=1 and
then use the -make-mdins and -use-mdins flags to modify the sander mdin
files directly. If the value of 1 suffices (as it usually does), just omit
ipb altogether.

For pure energies, I don't think the value of ipb will make much of a
difference. If you're doing dynamics with PB, then the functional form of
the dielectric boundary matters since you're computing gradients. But if
you're just computing solvation free energies, I doubt it will have a very
noticeable effect (hopefully someone can correct me if I'm misunderstanding


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jun 24 2015 - 05:30:03 PDT
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