AMBER Archive (2002)

Subject: Re: how to keep aromatic ring flat

From: Bill Ross (photoriot_at_yahoo.com)
Date: Fri Jun 14 2002 - 18:34:42 CDT

> A six-membered aromatic carbon ring is clearly
> distorted somehow after I run a few hundred steps of
> minimization with sander. But this ring should be
> almost flat in chemistry. I already use "improper"
on
> each sp2 carbon in its Prep file.

The IMPROPER section of the prep.in file no longer
has any effect, if you are using leap. Leap simply
matches the atom types in the topology to the
improper params in parm.dat and uses params that
apply.

It sounds like you are lacking parameters for one
or more of the impropers involved.

the IMPROPER section does have a debugging use in
leap - if you load a prep.in and saveamberparm, it
will use the prep impropers to check the ones that
are applied. I forget the details of what is shown.

Bill Ross

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