On Fri, Jun 21, 2013, Krisztina Feher wrote:
>
> I attached the tripeptide. I built it in Accelrys Discovery Studio
> Visualiser 3.5 and afterwards I cleaned geometry - whatever that means
> there.
>
> antechamber -i igc-dap+-dal_dsv.pdb \
Ugh...did you visualize this structure? It consists of two completely
separated fragments, with about a 4 Ang. distance between them. Antechamber
needs a "pretty good" (tm) to start from.
>
> In my experince the version 12 Antechamber is rejecting a lot molecules
> than the version 9.
We'd like to hear of results that the recent versions fail. However, the old
divcon code could prematurely signal convergence, appearing to work but
actually giving bad results. The current code should (properly) e unhappy
with the structure you provide (although it certainly might give better
diagnostics in the output.)
...dac
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Received on Sat Jun 22 2013 - 06:00:03 PDT
