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From: Steven <steven0122.gmail.com>

Date: Fri, 20 Jun 2008 22:11:08 +0800

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

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To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

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Received on Sun Jun 22 2008 - 06:07:52 PDT

Date: Fri, 20 Jun 2008 22:11:08 +0800

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:

The same format as the previous FF forces files is used for gaff.dat and

can be found here: http://ambermd.org/formats.html .

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

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....

Dr. Thomas Steinbrecher has given a nice answered here:

http://ambermd.org/Questions/vdwequation.pdf

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

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

to majordomo.scripps.edu

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" (in the *body* of the email)

to majordomo.scripps.edu

Received on Sun Jun 22 2008 - 06:07:52 PDT

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