Re: [AMBER] Parameters for selenocysteine

From: David A Case <>
Date: Thu, 10 Nov 2016 13:14:14 -0500

On Thu, Nov 10, 2016, David Case 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

Sorry: in my earlier email, I forgot that antechamber cannot handle selenium.

The "acdoctor" program prints out better error messages, and identifies
problems like this. We are in the process of incorporating acdoctor into
antechamber itself, so that a separate program is not needed.

[Scott: hope you are making progress on this. Be sure to get rid of the awful
yellow text that acdoctor puts out by default....]

> First, it is probably easiest to go to the R.E.D. webiste for this sort of
> problem.

I still think that the above suggestion is the most likely to work.


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Received on Thu Nov 10 2016 - 10:30:02 PST
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