Code:
# This file is fixpdb.awk.
# Useage awk -f fixpdb.awk [segid=wxyz] [chainID=X] <pdbfile.in >file.out
# [resname=abc]
# Extracts segments from pdb files and converts to a format acceptable by charmm.
# In command line can specify up to a four character segid with wxyz, e.g. prot. This
# field is ignored by current CHARMM versions, but needed for older versions.
# Can specify a one character chainID. If is specified on command line, extracts
# only lines whose character in column 22 matches chainID X. Use to extract specific
# subunit from pdb file.
# Instead, can specify a three character resname to select HOH or ligands like ARA.
# If resname is specified, extracts only lines whose resname in columns 18-20
# matches resname abc value.
# Writes header line as a remark.
# Ignores all other lines not beginning with ATOM or HETATM.
# If a single coordinate value for an atom is present, takes that.
# If multiple coordinates are present, signified by A, B, .. in column 17, takes only A.
# If protein and HOH lines are present and protein lacks a chainID, takes the
# protein lines only.
# Converts HOH to TIP and adds a 3, making TIP3, HIS to HSD, CD1 to CD_ for ILE,
# adds the segid in columns 73-76. Converts OXT or OCT1 to OT1 and OCT2 to OT2.
# Renumbers atoms starting from 1.
# Fields: Atom, Atom No, Space, Atom name, Alt Conf indic, Resname, Space,
# Chain Ident, Res Seq No, Spaces, x, y, z, Occup, Temp fact, Spaces, Segment ID
BEGIN {FIELDWIDTHS=" 6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 6 4"}
{
if ($1 == "HEADER")
print "REMARK" substr($0, 7, 69)
if ($1 != "ATOM " && $1 != "HETATM")
endif
else if ($5 != " " && $5 != "A")
endif
else if ($6 == resname || $8 == chainID || ($8 == " " && $1 != "HETATM"))
{
atomno++
if ($6 == "HOH")
{ $4 = " OH2"
$6 = "TIP"
$7 = "3"
}
if ($1 == "HETATM")
$1 = "ATOM "
if ($6 == "HIS")
$6 = "HSD"
if ($6 == "ILE" && $4 == " CD1")
$4 = " CD "
if ($4 == " OXT" || $4 == "OCT1")
$4 = " OT2"
if ($4 == "OCT2")
$4 = " OT1"
printf "%6s",$1
printf "%5d", atomno
printf "%1s", " "
printf "%4s", $4
printf "%1s", " "
printf "%3s", $6
printf "%1s", $7
printf "%1s", " "
printf "%4s", $9
printf "%4s", " "
printf "%8s", $12
printf "%8s", $13
printf "%8s", $14
printf "%6s", $15
printf "%6s", $16
printf "%6s", " "
printf "%4s\n", segid
}
}
END {printf "%3s\n", "END"}
03-29-2012
