> When "viewing" an AMBER topology file using the RDPARM utility one can list
> the dihedrals present using the 'dihedral' command. What do the letters B or E
> mean at the start of a dihedral line?
Yes, a bit of obscurity here... The rdparm.c code explains it a bit, but
it relates to how AMBER calculates the 1-4 nonbonded interactions.
Internally in the prmtop if the 4th atom is negative, this is an improper;
if the 3rd atom is negative, this means omit the 1-4...
I = improper (do not calculate 1-4)
E = neglect end-group interactions (do not calculate 1-4)
B = both (do not calculate 1-4)
= calculate 1-4
-- tec3
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun May 06 2007 - 06:07:30 PDT
