Hi,
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
attachment).
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
all).
Thanks,
Hannes.
--
Scanned by iCritical.
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- application/x-palm-database attachment: ring.pdb
Received on Wed Jul 17 2013 - 02:30:02 PDT
