Re: [AMBER] Parameters for selenocysteine

From: David A Case <>
Date: Thu, 10 Nov 2016 10:43:51 -0500

On Thu, Nov 10, 2016, Paul Meister wrote:
> I am trying to obtain parameters for a selenocysteine using antechamber. I
> have a Gaussian output file with the esp file and when I try to run
> antechamber, I get this error:
> For atom[7]:Se1, the best APS is not zero, bonds involved by this atom are
> frozen

First, it is probably easiest to go to the R.E.D. webiste for this sort of
problem. Second, the message often usually arises because of a bad geometry:
have you checked that? If it looks OK, you may have to post your Gaussian
output, plus details of how you created that.

(To help check where the problem lies, try running running antechamber with
am1-bcc charges, or even no charges; this will help to determine if the
problem is with the Gaussian output, or somewhere else.)


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Received on Thu Nov 10 2016 - 08:00:02 PST
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