Re: [AMBER] GBSA parameters

From: David A Case <>
Date: Sun, 28 Jan 2018 21:32:21 -0500

On Sun, Jan 28, 2018, Siddhartha Jain wrote:

> I wanted to know where the files that have the parameter sets are as I need
> to compute the Hessian of the MM-GBSA energy function. But it seems there
> might be a way to get the Hessian via the mme2 function in NAB?

The mme2 routines know how to calculate the Hessian for the original GB
model (igb=1). They has never been extended to the "OBC" or "Neck" variants
of GB. That would be an interesting, but complex, application of the chain
rule for derivatives: not hard in principle, but probably a pretty fair amount
of work. (Volunteers are welcome, but should recognize that the demand for
normal mode analyses for biomolecules is pretty limited. Most people
interested in this sort of analysis use quasi-harmonic analysis instead,
which doesn't require second derivatives.)

> if you have pointers on how to call that function in python...

Python would be a stretch. The "sff" routines are written in C, and the
current documented API is for NAB (a C-like language). In the next release of
AmberTools, we will also include and document the C API.


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Received on Sun Jan 28 2018 - 19:00:02 PST
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