Dear Amanda,
> I am scrutinizing my parmtop file and discovered that the
> ANGLE_EQUIL_VALUE is
> indeed listed in radians, despite documentation and newsgroup
> threads to the
> contrary, both of which indicate that ANGLE_EQUIL_VALUE
> should be in degrees.
> It is likewise for dihedrals. I double checked the angle
> equilibrium values in
> my parmtop file against the force field file (leaprc.gaff),
> and it is a match
> (except that the former is in radians and the latter in degrees).
Indeed, you are correct, the data in the prmtop file should all be in
radians, this is contary to the values specified in the parmxx.dat and any
frcmod files where the values should be in degrees. Leap converts the values
to radians when creating the prmtop file. It appears that page 286 of the
manual is incorrect. I have updated the errata page on the website.
Apologies...
> The GAFF file lists equilibrium angles in degrees, so
> somewhere in the creation
> of the parmtop file it must have been actively converted to radians.
Yes, this is correct... All files 'prior' to the prmtop should have all
angles (and dihedral phases) in degrees. When the prmtop is created these
will be converted to radians.
> Questions:
> * Was Leap/saveAmberParm updated at some point to save
> parmtop angles in radians?
It has always been this way, seems nobody spotted the error in the manual
before now.
> * Can I count on my parmtop file angles to be in radians, or
> will it depend on certain implementations?
It should always be in radians.
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Mar 26 2006 - 06:10:16 PST
