[AMBER] antechamber issues

From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Date: Wed, 17 Jul 2013 10:02:47 +0100


I have found two issues with antechamber:

1) When I convert the attached pdb file to mol2 with e.g.

antechamber -i ring.pdb -fi pdb -o ring.mol2 -fo mol2 -j 4 -s 2

I get a mol2 file with reasonable GAFF atom types.

But when I try to get a "standard" mol2 with Sybyl atom types via

antechamber -i ring.mol2 -fi mol2 -o ring-sybyl.mol2 -fo mol2 -at sybyl
-s 2 -j 4 (or -j 1)

I get wrong atom types (see attachment). The same happens when
directly converting from the PDB (identical mol2).

Converting the original pdb to mol2 with openbabel yield Sybyl atom
types that I would think are a reasonable match of the GAFF types (see

2) I would expect a command like

antechamber -i ring.pdb -fi pdb -o sqm.in -fo sqmcrt -j 0

to write the SQM input file but it doesn't (not output generated at

Scanned by iCritical.

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Received on Wed Jul 17 2013 - 02:30:02 PDT
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