[AMBER] Dummy atoms when running antechamber in B4 (sustiva) tutorial

From: Nikolay N. Kuzmich <nnkuzmich.gmail.com>
Date: Mon, 29 May 2017 16:08:32 +0300

Dear Amber users,

In Sustiva/B4 tutorial I ran antechamber to convert sustiva_new.pdb file
into sustiva.mol2 file and to compute the bcc charges.
When the mol2 file was loaded into xleap and checked, unexpectedly the
dummy atoms in structure were seen.
In the Unit editor the sustiva molecule looked quite strange - the were no
triple bond
and several new single bonds appeared.

Should I correct the mol2 file manually for further stages
and how did the dummy atoms evolve?
How one can avoid it in the future?

Kind regards,
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Received on Mon May 29 2017 - 06:30:03 PDT
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