Re: amber-developers: Question concerning wildcards in dihedral definitions.

From: David A. Case <>
Date: Wed, 29 Jun 2005 17:46:03 -0700

On Wed, Jun 29, 2005, Thomas E. Cheatham, III wrote:
> for parm94.dat:
> As far as PLEP goes, everything is equivalent to LEaP EXCEPT for change
> one improper:
> XXX I 32: 1.100 3.14 2.0 :1.N7 :1.N9 :1.C8 :1.H8
> (16,13,14,15)
> XXX B 47: 1.100 3.14 2.0 :1.N9 :1.N7 :1.C8 :1.H8
> (13,16,14,15)
> which alters the atom order. This does alter the energy by a small
> (due entirely to this torsion) but should not be disasterous for

Assuming(?) that the second one above is what LEaP gives, it is following
the rules in the code, but these are pretty arcane rules. In even the
short run, we should probably go to a correct improper term, that does not
depend upon the order of the peripheral atoms...

> With the new parm99 of DAC, the results are equivalent before and after
> the copy unit in LEaP, but now the energy does not agree with parm99.dat

> (either before or after the copy)
> as nine additional V3 torsions are added to the pre-copy original parm99

> results; OS-CT-CT-H1, OS-CT-CT-HC, H1-CT-CT-OH, i.e. torsions on H4',
> H2'? in addition to H3', H5'? we saw previously. This confuses me even
> more as why after the copy did LEaP not add the V3 to ALL the X-CT-CT-X
> interactions involving H i.e. only to H1-CT-CT-OS and NOT HC-CT-CT-OS or

> H1-CT-CT-OH?

See if parm99.dat.new2 fixes this. I think all of the three-fold torsions
see above should now be zeroed out.

Received on Wed Apr 05 2006 - 23:49:55 PDT
Custom Search