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
