VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Mar 30 2009 - 19:27:01 CDT

Got distracted by other work, and have just gotten back to the question of adding

heme to the dowser dictionary & parameters. I got one of the free distributions of gromos, and

put that up, & started looking through the ffgmx* files, as recommended on a link

from the dowser plugin page. To make sure I had the right thing, I started looking for values

identical to those listed for N:

 

This is in dowser:

 

REMARK atomtype LJ-a LJ-b MS-radius
TYPE N 49.36 1300.0 2.40 # any Nitorgen

While the closest thing I can seem to find is in ffmgxnb.rtp, where the apparently relevant

comment line reads:

 

;name at.num mass charge ptype c6 c12
& N reads:

    N 7 14.00670 0.000 A 0.24362E-02 0.16924E-05

Am I looking at the right thing? If so, how do I transmogrify the c6 & c12 values into those

in dowser?

 

Thanks!

Irene Newhouse

 

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