Re: [AMBER] Hybridization problem in Amber

From: David A Case <>
Date: Sun, 27 Aug 2017 17:08:55 -0400

On Fri, Aug 25, 2017, Julian Stys wrote:
> I am making a non-standard residue (Azide group attached to ALA residue),
> and I'm using missing parameters from both gaff.dat and parm99.dat. For
> nitrogens, I'm using (n1 14.01 0.530 Sp N), and so I added addAtomTypes{ {
> "n1" "N" "sp" } } in my leaprc script.
> The problem is that when I try to make the lib file, the hybridization
> changes to sp2 because all the nitrogen types in leaprc.gaff are sp2. It
> gives me the error: atom type n1 - unknown hybridization sp.

First: are you sure this is an error message? There are three places in
amber.c where the hybridization is checked, and only one of them allows "sp"
as an option (no idea why right now). But it's also not clear from a
quick look at the code that this message triggers any error.

In general, LEaP makes very little use of "hybridizations". You could try
setting n1 to sp2 in your leaprc file (as in leaprc.gaff) and see what
happens. Unless LEaP has to try to build systems with missing coordinates, it
doesn't look like type "sp" is every used.

Let us know what happens: at a first glance it appears to be an oversight
(bug) that hybridization "sp" is not being accepted.

...thanks for the report....dac

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Received on Sun Aug 27 2017 - 14:30:02 PDT
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