Sorry, that was my first failed attempt. I attached a correct pdb file. The CO carbon is assiged as "c2" by divcon and as "c1" by sqm in the output .mol2 file.
Krisztina
--------------------------------------------
On Sat, 6/22/13, David A Case <case.biomaps.rutgers.edu> wrote:
Subject: Re: [AMBER] GAFF atom type for CO
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Saturday, June 22, 2013, 2:48 PM
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 - 07:30:02 PDT
