AMBER Archive (2006)

Subject: Re: Re: Re: AMBER: bond parameters for positively charged guanidine group

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Thu Mar 09 2006 - 13:24:57 CST

Adding improper torsions to a prepin file will do *nothing* since
they are ignored by leap. You need to make sure that the atom
types of you NH2 and the C match an improper in the parameters.
The simple way is to look at the types in an NH2 group in an
existing residue and think about whether your types are correct
or whether you need to add an improper to your parameters. If you
do, best to make sure that it isn't picked up in another place
that you don't want it. If you load a prepin with an IMPROPER
section, leap will remember (but not use) them and will show
them on saveamberparm in a helpful way.

Bill
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