Charmm29 (I don’t know about more recent versions) labels many hydrogen atoms as HB1, HB2 etc. Rosetta however, looks for 1HB, 2HB etc. For most residues this causes no problems even though Rosetta can’t identify the hydrogens, however, a problem arises in the case of proline, as Rosetta misidentifies such residues as hydroxyproline. A simple fix is to massage a pdb derived from Charmm with the following awk script before reading it into Rosetta. The script also changes HSD and HSE to HIS and fixes an ILE atom name.
# This file is fixcharmm.awk and runs under linux.
# Useage: awk -f fixcharmm.awk fixed_charmmout.pdb.
# Charmm29 (Later versions may be better.) “mis” labels H’s, e.g. _HD1 rather than 1HD_ and causes Rosetta to misread proline as hydroxyproline.
# Relabels H’s from Charmm of PRO from, e.g. _HD1 to 1HD_
# Fixes label on atom CD1 of ILE.
# Relabels HSD and HSE from Charmm as HIS
BEGIN {FIELDWIDTHS=” 12 4 1 3 46″}
{
if ($2 == ” HD1″ && $4 == “PRO”)
$2 = “1HD “
if ($2 == ” HD2″ && $4 == “PRO”)
$2 = “2HD “
if ($2 == ” HB1″ && $4 == “PRO”)
$2 = “1HB “
if ($2 == ” HB2″ && $4 == “PRO”)
$2 = “2HB “
if ($2 == ” HG1″ && $4 == “PRO”)
$2 = “1HG “
if ($2 == ” HG2″ && $4 == “PRO”)
$2 = “2HG “
if ($2 == ” CD ” && $4 == “ILE”)
$2 = ” CD1″
if (($4 == “HSD”) || ($4 == “HSE”))
$4 = “HIS”
printf “%-12s”, $1
printf “%-4s”, $2
printf “%-1s”, $3
printf “%-3s”, $4
printf “%-46sn”, $5
}
.
