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From: Junmei Wang <jwang.encysive.com>

Date: Tue, 1 Mar 2005 12:57:49 -0600

The torsional angle term takes a form of (0.5) * Vn * (1 + cos (n*phi -

gamma)). Here, n takes 1, 2, 3, 4 ...; Vn is the force constant for the

nth Fourier term (the 3rd Field); gamma is the phase angle (4th Field);

n is in the 5th Field of a torsional angle term. If n is a negative

number, the immediately followed term is also applied for the same

torsional angle (more than one Fourier terms for this torsional angle).

On the other hand, if n is a positive number, the followed term is for

another torsional angle. I hope I made it clear.

Best

Junmei

==================================================

Dr. Junmei Wang

Chemistry & Biophysics

Encysive Pharmaceuticals Inc.

7000 Fannin, Houston TX 77030

Tel: 713-578-6649

Email: jwang.encysive.com

http://amber.scripps.edu/antechamber/antechamber.html

==================================================

Dear Amber Users,

I am calculating the diheral energy of a small molecule for

which I am using gaff.dat of Amber 8. I have noticed that some of the

dihedral are repeated with different values. for example

c3-c2-c2-c3 1 6.65 180.0 -2.

Junmei et al, 1999

c3-c2-c2-c3 1 1.90 180.0 1.

Junmei et al, 1999

c3-c3-c3-c3 1 0.18 0.0 -3.

Junmei et al, 1999

What basis is used for the calculation of such dihedral (whether

all or some are used) and how it is done in Amber.

Thanks

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Received on Tue Mar 01 2005 - 19:53:01 PST

Date: Tue, 1 Mar 2005 12:57:49 -0600

The torsional angle term takes a form of (0.5) * Vn * (1 + cos (n*phi -

gamma)). Here, n takes 1, 2, 3, 4 ...; Vn is the force constant for the

nth Fourier term (the 3rd Field); gamma is the phase angle (4th Field);

n is in the 5th Field of a torsional angle term. If n is a negative

number, the immediately followed term is also applied for the same

torsional angle (more than one Fourier terms for this torsional angle).

On the other hand, if n is a positive number, the followed term is for

another torsional angle. I hope I made it clear.

Best

Junmei

==================================================

Dr. Junmei Wang

Chemistry & Biophysics

Encysive Pharmaceuticals Inc.

7000 Fannin, Houston TX 77030

Tel: 713-578-6649

Email: jwang.encysive.com

http://amber.scripps.edu/antechamber/antechamber.html

==================================================

Dear Amber Users,

I am calculating the diheral energy of a small molecule for

which I am using gaff.dat of Amber 8. I have noticed that some of the

dihedral are repeated with different values. for example

c3-c2-c2-c3 1 6.65 180.0 -2.

Junmei et al, 1999

c3-c2-c2-c3 1 1.90 180.0 1.

Junmei et al, 1999

c3-c3-c3-c3 1 0.18 0.0 -3.

Junmei et al, 1999

What basis is used for the calculation of such dihedral (whether

all or some are used) and how it is done in Amber.

Thanks

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

The AMBER Mail Reflector

To post, send mail to amber.scripps.edu

To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Tue Mar 01 2005 - 19:53:01 PST

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