[gmx-users] various files generated using prodrg

h a y600100 at gmail.com
Wed Jul 9 14:08:43 CEST 2008

Dear users,

I used prodrg to generate topology in G43a1 force field, the set of files I
have are
DRGFIN.PDB  : the final PDB file with all hydrogens added
DRGPOH.PDB  : the final PDB file with only polar hydrogens added
DRGNOH.PDB  : the final PDB file without any hydrogens added

DRGFIN.MOL  : the final Molfile with all hydrogens added
DRGPOH.MOL  : the final Molfile with only polar hydrogens added
DRGNOH.MOL  : the final Molfile without any hydrogens added

DRGFIN.GRO  : final coordinates in GROMOS87 format (all hydrogens)
DRGPOH.GRO  : final coordinates in GROMOS87 format (polar hydrogens only)

DRGCNS.PAR  : CNS parameter file
DRGCNS.TOP  : CNS topology file


DRGSHX.TOP  : SHELX topology

DRGTRS.O    : O <9.0 torsion database (read in with: read DRGTRS.O in O)
DRGFNOH.O6  : O <9.0 refi dictionary
DRGNOH.O    : O 9.x dictionary


DRGWIF.TOP  : WHAT IF topology

DRGFIN.MOL2 : SYBYL2 file with all hydrogens
DRGPOH.MOL2 : SYBYL2 file with only polar hydrogens

DRGAD2.PDBQ : AutoDock 2.4 PDBQ file
DRGAD3.PDBQ : AutoDock 3.0 PDBQ file

DRGHEX.TOP  : HEX topology

Can anybody please explain what is this "what if topology","hex
topology","CNS parameters,topology" ??
and this "REFMAC5 library" ??

thanks a ton,

Harshith, UG,
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