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

Date: Sat, 18 Dec 2010 09:57:27 +0800

Dear Jason,

Thanks for your patient reply! I learned a lot from your meticulous

parse. However, i still have two questions about the torsion term.

I notice that there is a parameter in torsion torsion called phase angle,

in the manual of AMBER8 about "Parameter Development" , I guess the

phase angle determine where the torsion potential get its minimal point,is it right?

Besides, in my recent work, i need to simulate AdoMet (S-Adenosyl methionine;http://en.wikipedia.org/wiki/S-Adenosyl_methionine) that contains a positive charged sulfur atom.I find there is a paper supply the parameters of the special sulfur atom used in amber force filed implemented in the soft ware of Macromodel,But maybe there is some difference of the format

for torsion angle used in Macromodel and AMBER software.I found the

author only list the following parameters for the special torsion angle:

V1/2 V2/2 V3/2

SP-CT-CT-CT -1.6814 1.0698 -0.0001

I speculate that the PN (periodicity) should be 3, and the PK should be

-1.6814; 1.0698; -0.0001.But i can not speculate the phase angle of the three terms,meanwhile, i noticed that the PK parameters have two

negative values but there are no negative values about the PK in

parm99.dat .Therefore,I presume we can translate the listed parameters to the proper format can be used in AMBER software,Could you be so

kindly to tell me how to do that ? I have been confused for a whole week.

Thanks in advance!

Best regards!

Xiangqian Kong

Jason Swails <jason.swails.gmail.com> 在 Wed, 15 Dec 2010 09:55:56 写道：

*>Hello,
*

*>
*

*>On Wed, Dec 15, 2010 at 1:42 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
*

*>
*

*>
*

*>Think of this not as 3 different parameters, but rather 3 terms that compose
*

*>a single parameter. The negative periodicity at the end indicates that it's
*

*>a "multiterm" dihedral parameter.
*

*>
*

*>
*

*>> 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
*

*>
*

*>
*

*>In the Amber force field, it would be a mistake to try and glean chemical
*

*>insight out of the torsion parameters; in general there is none. Instead,
*

*>think of the torsion as a simple correction. This is because 1-4 non-bonded
*

*>interactions (which are interactions between atoms separated by 3 bonds; or
*

*>those that compose a dihedral angle) are included in the force field
*

*>(although the Amber force field does scale them). Therefore, part of the
*

*>torsion potential is already taken care of by other terms! Because the force
*

*>field is not *perfect* in this regard, however, and because there are
*

*>occasionally quantum mechanical effects (such as breaking conjugation in
*

*>certain conjugated systems) that can't be modeled by a classical, non-bonded
*

*>potential, the difference between the torsion potential accounted for by 1-4
*

*>terms and the *real* torsion potential (which you can calculate via
*

*>high-level quantum mechanical calculations, for instance) is what has to be
*

*>accounted for by the torsion terms. Long story short: no chemical meaning
*

*>behind torsion terms.
*

*>
*

*>
*

*>> 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 ?
*

*>>
*

*>
*

*>Yes. The torsion terms are simply a Fourier sum. Torsions are well-suited to
*

*>being fit with Fourier sums since they are periodic (clearly). As is always
*

*>true with any kind of expansion, if a function doesn't happen to be a single
*

*>term, then the more terms you include, the better fit you can get. That is
*

*>why many torsion parameters have multiple Fourier terms.
*

*>
*

*>Hope this helps,
*

*>Jason
*

*>
*

*> 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
*

*>>
*

*>
*

*>
*

*>
*

*>--
*

*>Jason M. Swails
*

*>Quantum Theory Project,
*

*>University of Florida
*

*>Ph.D. Graduate Student
*

*>352-392-4032
*

*>_______________________________________________
*

*>AMBER mailing list
*

*>AMBER.ambermd.org
*

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

*>
*

*>
*

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 Fri Dec 17 2010 - 18:00:03 PST

Date: Sat, 18 Dec 2010 09:57:27 +0800

Dear Jason,

Thanks for your patient reply! I learned a lot from your meticulous

parse. However, i still have two questions about the torsion term.

I notice that there is a parameter in torsion torsion called phase angle,

in the manual of AMBER8 about "Parameter Development" , I guess the

phase angle determine where the torsion potential get its minimal point,is it right?

Besides, in my recent work, i need to simulate AdoMet (S-Adenosyl methionine;http://en.wikipedia.org/wiki/S-Adenosyl_methionine) that contains a positive charged sulfur atom.I find there is a paper supply the parameters of the special sulfur atom used in amber force filed implemented in the soft ware of Macromodel,But maybe there is some difference of the format

for torsion angle used in Macromodel and AMBER software.I found the

author only list the following parameters for the special torsion angle:

V1/2 V2/2 V3/2

SP-CT-CT-CT -1.6814 1.0698 -0.0001

I speculate that the PN (periodicity) should be 3, and the PK should be

-1.6814; 1.0698; -0.0001.But i can not speculate the phase angle of the three terms,meanwhile, i noticed that the PK parameters have two

negative values but there are no negative values about the PK in

parm99.dat .Therefore,I presume we can translate the listed parameters to the proper format can be used in AMBER software,Could you be so

kindly to tell me how to do that ? I have been confused for a whole week.

Thanks in advance!

Best regards!

Xiangqian Kong

Jason Swails <jason.swails.gmail.com> 在 Wed, 15 Dec 2010 09:55:56 写道：

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 Fri Dec 17 2010 - 18:00:03 PST

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