Using the HSG Convention in tLeap / Amber

I have updated the leaprc.ff99 file so that the nomenclature of HSG and HG is mapped for the amino acid residue cysteine. This was done using the addPdbAtomMap command as shown below.

I am using .../dat/leap/lib/all_aminont02.lib and it has these lines:

!entry.NCYS.unit.atoms table str name str type int typex int resx int flags int seq int elmnt dbl chg
"N" "N3" 0 1 131072 1 7 0.190200
"H1" "H" 0 1 131072 2 1 0.205600
"H2" "H" 0 1 131072 3 1 0.205600
"H3" "H" 0 1 131072 4 1 0.205600
"CA" "CT" 0 1 131072 5 6 0.021300
"HA" "HP" 0 1 131072 6 1 0.057800
"CB" "CT" 0 1 131072 7 6 -0.031600
"HB2" "H1" 0 1 131072 8 1 0.065500
"HB3" "H1" 0 1 131072 9 1 0.065500
"SG" "SH" 0 1 131072 10 16 -0.246400
"HSG" "HS" 0 1 131072 11 1 0.159100 <--- Clue
"C" "C" 0 1 131072 12 6 0.683700
"O" "O" 0 1 131072 13 8 -0.581900

This is where I got the clue to use HSG and not HG

Following the advise of Bill Ross I added
addPdbAtomMap {
# Cysteine HSG convention
{ "HG" "HSG" }
}
and diff'ed the amber.pdb and prmtop file and got a
perfect match between the input PDB file using
HSG (the one I originally got to work) and
the HG (with addPdbAtomMap fix ).

Fortunetly the serine remained HG
so apparently the leap figured out that the HG to
HSG change only applied to the CYS

Thanks very much JWCraft

PS actually all the libs had the HSG convention

11% pwd
.. AMBER/IRIX64/amber7/dat/leap/lib
12% grep HSG *
all_aminoct02.lib: "HSG" "HS" 0 1 131072 9 1 0.157700
all_aminoct02.lib: "HSG" "HS" 0 -1 0.0
all_aminoct02EP.lib: "HSG" "HS" 0 1 131072 11 1 0.161700
all_aminoct02EP.lib: "HSG" "HS" 0 -1 0.0
all_aminoct91.lib: "HSG" "HS" 0 1 131072 9 1 0.135000
all_aminoct91.lib: "HSG" "HS" 0 -1 0.0
all_aminoct94.lib: "HSG" "HS" 0 1 131072 9 1 0.206800
all_aminoct94.lib: "HSG" "HS" 0 -1 0.0
all_aminont02.lib: "HSG" "HS" 0 1 131072 11 1 0.159100
all_aminont02.lib: "HSG" "HS" 0 -1 0.0
all_aminont02EP.lib: "HSG" "HS" 0 1 131072 13 1 0.164200
all_aminont02EP.lib: "HSG" "HS" 0 -1 0.0
all_aminont91.lib: "HSG" "HS" 0 1 131072 11 1 0.135000
all_aminont91.lib: "HSG" "HS" 0 -1 0.0
all_aminont94.lib: "HSG" "HS" 0 1 131072 11 1 0.197500
all_aminont94.lib: "HSG" "HS" 0 -1 0.0
pro-dna91.nmr.off: "HSG" "HS" 0 1 131072 9 1 0.135000
pro-dna91.nmr.off: "HSG" "HS" 0 -1 0.0
pro-dna91.nmr.off: "HSG" "HS" 0 1 131072 11 1 0.135000
pro-dna91.nmr.off: "HSG" "HS" 0 -1 0.0