Dear Nilov,
Thank you very much！I learned a lot in the AMBER 8 manual.
Best regards!
Xiangqian Kong
Dmitry Nilov <nilovdm.gmail.com> 在 Wed, 15 Dec 2010 10:21:24 写道：
>Hello!
>Load Amber8 manual from http://ambermd.org, and in "Parameter
>development" section you will find the explanation.
>
>On Wed, Dec 15, 2010 at 9:42 AM, xqkong <xqkong.mail.shcnc.ac.cn> wrote:
>> 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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>>
>
>
>
>--
>Dmitry Nilov,
>Lomonosov Moscow State University
>
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>
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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Received on Fri Dec 17 2010 - 18:30:04 PST
