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From: xqkong <xqkong.mail.shcnc.ac.cn>

Date: Wed, 15 Dec 2010 14:42:19 +0800

Dear amber users,

As a novice of amber, i have some questions about the torsion parameters in parm99.dat. I noticed that sometimes there are more than one line of torsion parameters corresponding to the given atom types.Such as

CT-CT-CT-CT 1 0.18 0.0 -3.

CT-CT-CT-CT 1 0.25 180.0 -2.

CT-CT-CT-CT 1 0.20 180.0 1

Therefore, I have the following questions,

First of all ,why do we need three kinds of parameters to describe a given torsion angle ? what does the chemical meaning of this configuration ?I noticed that the difference in the periodicity range from 3 to 1.But we

know that when we rotate a bond consists of four sp3 carbons from 0 to 360 degree, the number of the maximum energy should be 3. so the

periodicity should be 3 rather than 2 or 1.

Secondly, How does the program such as sander to use these

parameters in the simulation? In amber force field , the torsion energy was

defined as follow,

ET=sum{Vn/(2*idiv)*(1+cos(|pn|*phi-phase)}

Taking the CT-CT-CT-CT as an example, should the total torsional

energy for this dihedral be

E(torsion for CT-CT-CT-CT )

= ( pk1*(1 + Cos[pn1*phi - phase1]) + pk2*(1 + Cos[pn2*phi - phase2]) + pk3*(1 + Cos[pn3*phi - phase3]) ).where pk1 = 0.20; pk2 = 0.25; pk3 = 0.18; phase1 = Pi; phase2 = Pi; phase3 = 0; pn1 = 1; pn2 = 2; pn3 = 3 ?

Any suggestions will be greatly appreciated!

Best regards,

Xiangqian Kong

Drug Design and Discovery Center,

Shanghai Institute of Materia Medica,

The Chinese Academy of Sciences,

Shanghai 201203,P. R. China

Email: xqkong.mail.shcnc.ac.cn

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AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Dec 14 2010 - 23:00:03 PST

Date: Wed, 15 Dec 2010 14:42:19 +0800

Dear amber users,

As a novice of amber, i have some questions about the torsion parameters in parm99.dat. I noticed that sometimes there are more than one line of torsion parameters corresponding to the given atom types.Such as

CT-CT-CT-CT 1 0.18 0.0 -3.

CT-CT-CT-CT 1 0.25 180.0 -2.

CT-CT-CT-CT 1 0.20 180.0 1

Therefore, I have the following questions,

First of all ,why do we need three kinds of parameters to describe a given torsion angle ? what does the chemical meaning of this configuration ?I noticed that the difference in the periodicity range from 3 to 1.But we

know that when we rotate a bond consists of four sp3 carbons from 0 to 360 degree, the number of the maximum energy should be 3. so the

periodicity should be 3 rather than 2 or 1.

Secondly, How does the program such as sander to use these

parameters in the simulation? In amber force field , the torsion energy was

defined as follow,

ET=sum{Vn/(2*idiv)*(1+cos(|pn|*phi-phase)}

Taking the CT-CT-CT-CT as an example, should the total torsional

energy for this dihedral be

E(torsion for CT-CT-CT-CT )

= ( pk1*(1 + Cos[pn1*phi - phase1]) + pk2*(1 + Cos[pn2*phi - phase2]) + pk3*(1 + Cos[pn3*phi - phase3]) ).where pk1 = 0.20; pk2 = 0.25; pk3 = 0.18; phase1 = Pi; phase2 = Pi; phase3 = 0; pn1 = 1; pn2 = 2; pn3 = 3 ?

Any suggestions will be greatly appreciated!

Best regards,

Xiangqian Kong

Drug Design and Discovery Center,

Shanghai Institute of Materia Medica,

The Chinese Academy of Sciences,

Shanghai 201203,P. R. China

Email: xqkong.mail.shcnc.ac.cn

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Dec 14 2010 - 23:00:03 PST

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