RE: AMBER: from dihe parameters to torsional energy

From: Ross Walker <>
Date: Wed, 17 Dec 2008 09:28:21 -0800

Hi Ilyas,

> > 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.
> 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).

I haven't strictly checked the code but my understanding is that this is not
a problem. The code checks to see what the phase value is and then uses the
appropriate equation form:

Granted the code is 'horrendous' to say the least but here is some examples:

     iper = int(dabs(pn(ic))+0.0001)
     if(iper == int(dabs(pn(ic))-0.0001)) goto 400
     if(iper > 6 .or. iper < 1) goto 400
     goto (30,35,40,45,50,55),iper
     if(dabs(3.14159d0-phase(ic)) < 0.01) goto 65

Etc etc. The net result of this (I believe) is that it doesn't matter what
the phase angle is it just does the calculation in alternative ways
depending on what the values are. There is of course the argument that a
phase of something other than 0 or 180 is techincally non-physical (maybe 90
is okay?) because the function is then no longer symmetric about 0 and so
there is effectively a hysteresis as one twists a dihedral through 360
degrees, however, the equation and code has no way of recording how many
rotations a dihedral has gone through.

Note this is nmode we are talking about here. Sander uses different code
which I believe uses the same algorithmic approach regardless of the value
of phase etc.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Fri Dec 19 2008 - 01:10:23 PST
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