[AMBER] How do you know when to include improper dihedrals????

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Mon, 12 Apr 2010 14:30:07 -0500

Dear amberers,

I guess my question is more to Ross Walker, since he is the one whose
parameterized NAD+ files I am referring to, but I'll accept a clarification
from anyone! :-)

Using the .mol2 file with charges and amber atomtypes for NAD+ with parmchk
and the parm99.dat file, a frcmod file is created that contains improper
dihedrals for the aromatic adenine ring system. Yet, in the frcmod file
provided by Ross Walker, there are no such improper dihedrals specified.

First let me say that I am not implying a mistake on Ross's part, because
I've seen a few other instances where this is the case also.

So my question is, when are the impropers that are supplied in the frcmod
file produced by parmchk not necessary?

For example, I have a compound I am parameterizing that contains planar
amides and planar thioester linkages. Using parmchk with the parm99.dat file
gives me impropers in the frcmod file with for each of these, with a large
force constant of 10.5.

Do I need these specifications for these planar linkages??
How do you decide???

Thanks so very much for your help in advance.

With regards,


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Received on Mon Apr 12 2010 - 13:00:02 PDT
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