Re: [AMBER] Fw: converts CA carbons to calcium atoms when doing the mol2 to pdbqt format conversion

From: David A Case <>
Date: Thu, 3 Sep 2020 16:36:59 -0400

On Wed, Sep 02, 2020, Esposito Carmen wrote:
>pythonsh -l file.mol2 -C -o file.pdbqt
>However, I noticed that when doing the format conversion carbon atoms
>with the atom type CA (in the mol2) are transformed into calcium atoms
>(Ca, in the pdbqt file).

I don't have an answer, but will note that is an
autodock script, not an Amber one. You may have better luck contacting
the AutoDock folks. I'll just note that the "pdbqt" files look a little
like PDB files, but are very non-standard, and seem to be using the
element columns for something quite different. I suspect that these
files may only be useful inside the AutoDock environment.

(Of course, someone on this list may also be able to help.)


AMBER mailing list
Received on Thu Sep 03 2020 - 14:00:02 PDT
Custom Search