Re: [AMBER] MMPBSA (inp=1 or inp=2)??

From: Ray Luo <>
Date: Fri, 15 Jul 2016 13:27:42 -0700

Hi AT,

On Fri, Jul 15, 2016 at 8:53 AM, Thakur, Abhishek <> wrote:
> Hi I am doing MMPBSA calculation
> I need some help to figure out that I should use inp=2 or inp=1 in PB.

First thing first, please use the latest version AmberTools 16 so some
of the error messages may not occur again.

Regarding your question on the differences of INP=1 or 2, why not try
both and study for yourself which one is better? In our own testing,
INP=2 agrees with experimental relative affinities better, i.e. RMSD
is smaller, though the correlations are similar. There are reports
that INP=2 does not work well in reproducing absolute affinities of
"large" ligands (i.e. protein/protein interactions), but I don't see
any analysis of its performance on relative affinities in
protein/protein interactions.

> Moreover some place I can see people using script for PB analysis in
> istrng=0.100, prbrad=1.4, radiopt=0, inp=2,
> indi=1.0, exdi=80.0, sander_apbs=0, scale=2.0,
> cavity_surften=0.0378, cavity_offset=-0.5692
> /
> At some place
> istrng=0.100,
> inp=2, radiopt=0
> /
> At manual
> istrng=0.100,
> /
For beginners, please just use the default options as set by the
script, as in the later two examples. You can certainly experiment
different options after gaining more experience in the method. These
options are documented in the manual on the mmpbsa scripts, or the
PBSA and SANDER programs.

> So I am unable to find out what are other terms for, moreover I am seeing if I go with manual and does not use inp=1 or 2 then I get an error
> PB Bomb in pb_aaradi(): No radius assigned for atom 66 CB 2C

The error you see is due to the use of radiopt=1 for PB calculations.
If you use radiopt=0 or if you use the gaff lower case atom types for
ligands, you won't see these errors. Also, in the newer versions of
AmberTools, INP=1 or INP=2 is no longer related to the radiopt option.
And I think the default radiopt is set to 0, reading the radii from
the prmtop files.

All the best,

Ray Luo, Ph.D.
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
> So now I am confused which script to follow, first one or second one, as the script given in manual is giving error.
> Moreover among those two script I should use inp =1 or inp=2 that also concerns me.
> As I cannot find what is difference between both of them.
> Thanking you,
> -AT
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Received on Fri Jul 15 2016 - 13:30:02 PDT
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