AMBER Archive (2008)

Subject: Re: AMBER: questions about gaff

From: Mark Williamson (mark.williamson_at_imperial.ac.uk)
Date: Wed Jun 18 2008 - 21:35:42 CDT

yzhao wrote:
> Recently I'm going to implement gaff to calculate system energy and do some
> energy minimization. I've read the paper "Development and testing of a general
> amber force field", however it didn't mention the meaning of the parameters
> in gaff.dat file.

The same format as the previous FF forces files is used for gaff.dat and
can be found here: http://ambermd.org/formats.html .

> Can anyone give me a guide on how to calculate the total energy
> based on these parameters.

The functional form for the total potential energy is the same as it was
in the original Cornell paper:

http://dx.doi.org/10.1021/ja00124a002

> I paste several line in the gaff.dat and the following is my current knowledge
> about the parameters. There are still some parameters that I can't understand.

> I'm much confusing about this part. How to use these parameter to calcuate Etorsion?
> Why the second column does not exist in certain torsion such as "c2-c3-c2-hc"? What
> is the function of second column when calcuate Etorsion and what is the meaning of positive
> and negative n?

This is also covered in http://ambermd.org/formats.html , it's an
indication to the program that the final torsion function is a
superposition of multiple cos terms, hence keep parsing in....

> d = distance(i,j); a = d/(ri + rj); Eab = sqrt(Ea*Eb);
> Evdw = Eab*(1.0 / a^12 - 2.0 / a^6)
> vdw r E
> h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
> h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
> h3 1.1870 0.0157 Veenstra et al JCC,8,(1992),963

Dr. Thomas Steinbrecher has given a nice answered here:
http://ambermd.org/Questions/vdwequation.pdf

> By the way, I also find some duplicate parameter terms in the gaff.dat that I listed in
> the attching file "Duplicate.txt". Some questions are also listed in it.

I'm not sure what to make of these... what version of AMBER are you
using? Have you applied any bug fixes specific for that version? I do
recall there being some duplicate gaff entry fixes in:

http://ambermd.org/bugfixes/8.0/bugfix.28

regards,

Mark
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