AMBER Archive (2008)

Subject: Re: Re: AMBER: questions about gaff

From: Steven (steven0122_at_gmail.com)
Date: Fri Jun 20 2008 - 09:11:08 CDT

I've got it. Thank you ever so much!
now I do a summary about it.

using gaff to calculate energy:
BOND Stretching Energy
Ebond = kr*(r-r0)^2
a1 a2 kr r0
#######################
ow-hw 553.0 0.9572
br-br 123.2 2.542
br-c 240.3 1.946

ANGLE Bending Energy
Eangle = kth*[(th-th0)*pi/180.0]^2
a1 a2 a3 kth th0
#############################
hw-ow-hw 100. 104.52
hw-hw-ow 0. 127.74
br-c -br 66.9 113.10

TORSION Energy
Etorsion = ((Vn/2)/npth) * [ 1 + cos( |n| * phi - gamma ) ]
a1 a2 a3 a4 npth Vn/2 gamma n
#############################################
X -c -c -X 4 1.200 180.000 2.000
X -c -c1-X 2 0.000 180.000 2.000
X -c -cg-X 2 0.000 180.000 2.000

IMPROPER TORSION Energy
Etorsion = (Vn/2) * [ 1 + cos( |n| * phi - gamma ) ]
a3 is the center sp2 carbon or nitrogen whose gaff type
is c/c2/ca/n/n2/na. phi is the torsion of a1-a2-a3-a4.
a1 a2 a3 a4 Vn/2 gamma n
##############################################
X -o -c -o 1.1 180. 2.
X -X -c -o 10.5 180. 2.
X -X -ca-ha 1.1 180. 2.

Van Der Waals Energy
d = distance(i, j); a = d / ( ri + rj ); Eij = sqrt( Ei * Ei );
Evdw = Eij*(1.0 / a^12 - 2.0 / a^6)
or Aij = Eij / ( ri + rj )^12; Bij = 2.0 * Eij / ( ri + rj )^6
Evdw = Aij / d^12 + Bij / d^6
  a1 r E
#################################################################
  h1 1.3870 0.0157
  h2 1.2870 0.0157
  h3 1.1870 0.0157

Electrostatic Energy
without explicit solvent using a distance-dependent
dielectric constant ( epsi = Rij ) )
with explicit solvent using a constant-dependent
dielectric constant ( epsi = 1.0 ) )
Eele = Qi*Qj/epsi*Rij;

Note:
 1. Torsion energy is the sum of general torsion and improper torsion energy.
 2. VDW and ELE energy differentiate 1-4 and 1-N (N>4) interaction.
    1-4 VDW energy should take a scale factor 1/2.0 and 1-4 electrostatic
    energy should take a scale factor 1/1.2.

If there are some mistakes, please help me to correct it. Thanks!

Best Regard,

Steven
2008-06-20

----------------------------------------------------------------------------
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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