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).
Using Amber 8 on Irix 6.5, for some file "foo":
1. I used Antechamber to create a prep file:
<< $AMBERHOME/exe/antechamber -i foo.mop -fi mopint -o foo.prepin -fo
prepi -c bcc -s 2 -mk "CARTESIAN AM1 STANDARD DIRECT OPT=LBFGS XTEST=0.0001" >>
2. I created my parmtop file with Leap, using GAFF/ Generalized Amber Force
Field:
<< saveAmberParm MOL foo.prmtop foo.inpcrd >>
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.
Here is the relevant part of my resulting parmtop file:
%FLAG ANGLE_EQUIL_VALUE
%FORMAT(5E16.8)
2.08846188E+00 1.90974009E+00 1.86401244E+00 2.17572838E+00 1.91811767E+00
2.14483604E+00 1.99299233E+00 2.25339556E+00 2.15967134E+00 1.99299233E+00
Questions:
* Was Leap/saveAmberParm updated at some point to save parmtop angles in
radians?
* Can I count on my parmtop file angles to be in radians, or will it depend on
certain implementations?
* Or should this really be in degrees, so the appearance of radians is in error?
Any help is greatly appreciated!
--Amanda
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Received on Sun Mar 26 2006 - 06:10:16 PST
