AMBER Archive (2008)

Subject: AMBER: questions about gaff

From: yzhao (yzhao_at_mail.sioc.ac.cn)
Date: Wed Jun 18 2008 - 21:01:45 CDT

Hi Amber Admin,

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

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.
Please help me to correct each energy equation base on the parameters. Thanks!

       molecular
        weight ?? ?? -- Is it not used when calculating energy?
c 12.01 0.616 Sp2 C carbonyl group
c1 12.01 0.360 Sp C
c2 12.01 0.360 Sp2 C
c3 12.01 0.878 Sp3 C

Ebond = kr*(r-r0)^2
bond kr r0
ow-hw 553.0 0.9572 TIP3P water
br-br 123.2 2.542 SOURCE1 4 0.0000 0.0000
br-c 240.3 1.946 SOURCE2 2 0.0285 0.0285

Eangle = kth*[(th-th0)*pi/180.0]^2
angle kth th0
hw-ow-hw 100. 104.52 TIP3P water
hw-hw-ow 0. 127.74 (found in crystallographic water with 3 bonds)
br-c -br 66.9 113.10 SOURCE0 1
br-c -c3 63.3 110.74 SOURCE3 1 0.0000 0.0000

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?

Etorsion = 0.5 * Vn * [ 1 + cos( n * phi - gamma ) ] ---- ( I guess )
torsion ?? Vn 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 same as X-c-c1-X
c3-c3-os-c 1 0.383 0.0 -3. Junmei et al, 1999
c3-c3-os-c 1 0.80 180.0 1. Junmei et al, 1999
c3-os-c3-os 1 0.10 0.0 -3. Junmei et al, 1999
c2-c3-c2-hc 1.1 180. 2. Junmei et al.1999
c2-c3-ca-hc 1.1 180. 2. Junmei et al.1999
c2-hc-c -o 1.1 180. 2. Junmei et al.1999

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

I also attached a txt file of the previous data if it can not be read clearly in the E-mail.

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.

Best Regards,

Steven

State Key Lab of Bio-organic and Natural Products Chemistry
Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences.
Addr. 354, Fenglin Road, Shanghai, China.
Tel.: +86-21-54925275
Email: yzhao_at_mail.sioc.ac.cn


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