Hi,
I noticed some erroneous behavior with parmchk/parmchk2 while trying to produce a full set of gaff (and gaff2) parameters for a molecule with a nitrophenyl group.
These two commands produce a slightly different output (besides the order of the parameters), with the nitro group improper “ca o no o” missing in the first case.
$ parmchk2 -f mol2 -i pxn.mol2 -a Y -o pxn.frcmod
$ parmchk2 -f prepi -i pxn.prepi -a Y -o pxn.frcmod
(This command was used to convert mol2 to prep::
$ antechamber -fi mol2 -i pxn.mol2 -fo prepi -o pxn.prepi)
According to parmchk2.c, in the latter case the impropers are read from the prepi (or prepc) file, while with mol2 (or ac), an improper is defined when the central atom has the improper field set to 1 in the PARMCHK.DAT file (or ATCOR.DAT in case of parmchk). In this file, the improper field for atom “no” is set to 0. When changing to 1, the improper is indeed printed out.
I attached pxn.mol2 and pxn.prepi.
Best,
--
Miha Purg
PhD Candidate
Department of Cell and Molecular Biology (ICM)
Uppsala University
BMC, Box 596
S-751 24 Uppsala
Sweden
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Received on Wed Sep 21 2016 - 00:30:03 PDT
