[AMBER] Misleading leaprc with ff12

From: Jesper Sørensen <jesorensen.ucsd.edu>
Date: Thu, 25 Oct 2012 10:00:24 -0700

Dear all,

The header of the leaprc.ff12 is misleading and it is leading to some confusion for users.
It states that loading the files gives you ff99SB for proteins, but in reality it is also loading frcmod.ff12SB further down (excerpts of the file shown at the bottom).

While this can be understood by reading the manual in detail, I think it is misleading for users just reading the header and loading the file into LEaP.
You could say, well who would do such as thing (said differently, who would not read the manual and/or the file in detail) - but really I think a significant number of users would!

Is this something that can/should be changed/bug-fixed?

logFile leap.log
# ----- leaprc for loading the ff12SB force field
# ----- NOTE: this is designed for PDB format 3!
# ff10 = ff99SB for proteins; ff99bsc0 for DNA; ff99sbsc_chiOL3 for RNA
frcmod12SB = loadamberparams frcmod.ff12SB

All the best,

Jesper Sørensen, Ph.D.
Postdoctoral Researcher, Amarolab
Department of Chemistry and Biochemistry
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093-0340
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Received on Thu Oct 25 2012 - 10:30:04 PDT
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