$FFPDB group (optional, relevant if QuanPol is used)
Simply pasting a PDB text file into $FFPDB may work.
(1). H atoms must be added beforehand, and must appear
at the correct places in the PDB file. Currently
QuanPol cannot add any missing atoms. The CHIMERA
program from UCSF can be used to add H atoms and
generate PDB files for QuanPol use.
(2). PDB format is enforced. Sequential numbers are not
used by QuanPol. Chemical symbols are used.
(3). Multiple chains are allowed. 'TER' lines can be used,
but not necessary.
(4). SSBOND lines are required to define S-S bonds.
(5). Most PDB metal ions can be processed by QuanPol and
assigned integer charges, Lennard-Jones potential and
effective QMREP potential. No bonds, angles and
dihedral angles will be assigned to them by QuanPol.
(6). Water section must be the last section of the PDB.
The potential of these waters is set by ITYPWAT.
A hydroxyl group can be obtained by manually editing
a water (can be purposely moved to be the last atom
of the PDB file) in the QuanPol generated $FFDATA.
(7). Small molecules in PDB should be processed separately
and recombined using ICOMBIN=1, 2, or 3.
Use a $END line to end $FFPDB.
The remaining groups apply only to MCSCF and CI runs.
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For hints on how to do MCSCF and CI
see the 'further information' section
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39 lines are written.
Edited by Shiro KOSEKI on Tue May 17 15:19:38 2022.