AMBER Archive (2007)

Subject: Re: AMBER: B or E Dihedral Labels in RDPARM output

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Fri May 04 2007 - 10:24:07 CDT

> 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

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