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From: Ilyas Yildirim <yildirim.pas.rochester.edu>

Date: Wed, 17 Dec 2008 12:10:13 -0500 (EST)

*> 1>. e = pk(ic) * (1.0+phase*cos(pn(ic)*phi)
*

*> where phase = 1.0 or -1.0, and pn = 1,2,3,4, or 6
*

*> 2>. e = pk*( 1.0+cos(pn*phi-phase) ----- the old energy form,
*

*> if phase angle is other than 0 or pi then assume this angle.
*

Ross,

I do not think that the 1st equation is used to do the energy

calculations of dihedrals. I did not check the source code for

this, but people published new dihedral parameters, which have phase

angles other than 0 or 180 (amber barcelone force field).

Here is a link to the frcmod file for the barcelone force field:

http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0

If the above equation is used to do the energy calculations, then

this means that amber force field does not allow to have phase angles

other than 0 or 180.

The first equation is used in nmode/ephi.f file. I will be very surprised

if the amber torsional energies are calculated this way in sander/pmemd.

nmode is used for normal-mode analysis (entropy calculations). It looks

like that if the phase is something other than 0 or 180, nmode will not

calculate the right torsional energy.

On Wed, 17 Dec 2008, Ross Walker wrote:

*> Dear Jeffrey,
*

*>
*

*>
*

*>
*

*> My understanding of this is that the two equations are the same thing given
*

*> certain conditions with respect to phase.
*

*>
*

*>
*

*>
*

*> The 'real' equation as written in terms of the AMBER force field is:
*

*>
*

*>
*

*>
*

*> e = pk(1.0+cos(pn*phi-phase))
*

*>
*

*>
*

*>
*

*> If my trigonometry is correct (it is early in the morning so buyer beware),
*

*> The cos term can be expanded here as:
*

*>
*

*>
*

*>
*

*> e = pk(1.0+cos(pn*phi)*cos(-phase))
*

*>
*

*>
*

*>
*

*> You would not want to do this computationally since cos functions are
*

*> expensive, however, in the case of phase = 0 then cos(-0) = 1 and if phase =
*

*> 180 then cos(-180) = -1
*

*>
*

*>
*

*>
*

*> Hence the above equation becomes:
*

*>
*

*>
*

*>
*

*> e = pk(1.0(+/-)cos(pn*phi))
*

*>
*

*>
*

*>
*

*> The net result though is that it is the same function as the original
*

*> definition above. Hence it should yield the same results. I don't know for
*

*> sure but I suspect that it is written this way either to make the
*

*> derivatives easier to express or compute or that the standard way of writing
*

*> it has some kind of instability / accuracy issue in certain circumstances,
*

*> i.e. when the dihedral gets close to either 0, 90 or 180.
*

*>
*

*>
*

*>
*

*> Hence the short answer is that it shouldn't matter which route through the
*

*> code gets taken here - in both cases you should end up with the same answer.
*

*>
*

*>
*

*>
*

*> If you want a list of dihedrals from the prmtop then you can run:
*

*>
*

*>
*

*>
*

*> $AMBERHOME/exe/rdparm prmtop
*

*>
*

*>
*

*>
*

*> and type 'dihedrals'
*

*>
*

*>
*

*>
*

*> This will list everything from which given a set of coordinates and the
*

*> original equation at the top above you should end up with the same energy as
*

*> is calculated using the expanded terms above.
*

*>
*

*>
*

*>
*

*> I hope that helps,
*

*>
*

*> All the best
*

*>
*

*> Ross
*

*>
*

*>
*

*>
*

*> From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
*

*> Jeffrey
*

*> Sent: Wednesday, December 17, 2008 1:15 AM
*

*> To: amber.scripps.edu
*

*> Subject: AMBER: from dihe parameters to torsional energy
*

*>
*

*>
*

*>
*

*> Dear all,
*

*>
*

*>
*

*>
*

*> I would like to figure out how dihedral parameters are used to
*

*> calculate the torsional energy. After checking the subroutine subroutine
*

*> ephi (src/nmode/ephi.f), I found two expressions were adopted for the
*

*> dihedral energy:
*

*>
*

*> 1>. e = pk(ic) * (1.0+phase*cos(pn(ic)*phi)
*

*> where phase = 1.0 or -1.0, and pn = 1,2,3,4, or 6
*

*> 2>. e = pk*( 1.0+cos(pn*phi-phase) ----- the old energy form,
*

*> if phase angle is other than 0 or pi then assume this angle.
*

*>
*

*>
*

*>
*

*> Taking CT-CT-CT-CT in parm99.dat as an example,
*

*>
*

*> CT-CT-CT-CT 1 0.18 0.0 -3. Junmei et al,
*

*> 1999
*

*> CT-CT-CT-CT 1 0.25 180.0 -2. Junmei et al,
*

*> 1999
*

*> CT-CT-CT-CT 1 0.20 180.0 1. Junmei et al,
*

*> 1999
*

*>
*

*>
*

*>
*

*> should the total torsional energy for this dihedral be one of the two forms:
*

*>
*

*> a. (pk1*(1 + phase*Cos[pn1*phi ]) + pk2*(1 + phase*Cos[pn2*phi ]) + pk3*(1
*

*> + phase*Cos[pn3*phi]))
*

*>
*

*> b. (pk1*(1 + Cos[pn1*phi - phase1]) + pk2*(1 + Cos[pn2*phi - phase2]) +
*

*> pk3*(1 + Cos[pn3*phi - phase3]))
*

*>
*

*>
*

*>
*

*> where pk1 = 0.18; pk2 = 0.25; pk3 = 0.20; phase1 = 0; phase2 = Pi; phase3 =
*

*> Pi; pn1 = 1; pn2 = 2; pn3 = 3;
*

*>
*

*> phase=1 or -1
*

*>
*

*>
*

*>
*

*>
*

*>
*

*> Another question is how to output each energy term in AMBER to check if I
*

*> have assigned a correct form of the expression?
*

*>
*

*>
*

*>
*

*> Any suggestion is greatly appreciated.
*

*>
*

*> Thanks very much for your time.
*

*>
*

*>
*

*>
*

*> -------
*

*>
*

*> Jeffrey
*

*>
*

*>
*

*>
*

*>
*

*>
*

*>
*

Date: Wed, 17 Dec 2008 12:10:13 -0500 (EST)

Ross,

I do not think that the 1st equation is used to do the energy

calculations of dihedrals. I did not check the source code for

this, but people published new dihedral parameters, which have phase

angles other than 0 or 180 (amber barcelone force field).

Here is a link to the frcmod file for the barcelone force field:

http://mmb.pcb.ub.es/PARMBSC0/frcmod.parmbsc0

If the above equation is used to do the energy calculations, then

this means that amber force field does not allow to have phase angles

other than 0 or 180.

The first equation is used in nmode/ephi.f file. I will be very surprised

if the amber torsional energies are calculated this way in sander/pmemd.

nmode is used for normal-mode analysis (entropy calculations). It looks

like that if the phase is something other than 0 or 180, nmode will not

calculate the right torsional energy.

On Wed, 17 Dec 2008, Ross Walker wrote:

-- Ilyas Yildirim, Ph.D. --------------------------------------------------------------- = Hutchison Hall B#10 - Department of Chemistry = = - University of Rochester = = 585-275-6766 (office) - = = http://www.pas.rochester.edu/~yildirim/ = --------------------------------------------------------------- ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Fri Dec 19 2008 - 01:09:59 PST

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