1PDB (pdb
code) ALT
(extension for alternative conformation, eg. 192A, 192B,...) current
directory: /data/
convert.sh
split original pdb-file into protein
and ligand, select all alternative conformations
required programs: pdbconv pymol (or other structure viewer)
input:
./data/1PDB/1PDB.pdb
/exports/scratch/stefan/ED/1PDB.ccp4 (optional, 2fo-fc electron density
maps in ccp4 format)
/exports/scratch/stefan/ED/1PDB.diff (optional, fo-fc electron density
maps in ccp4 format)
output:
./data/1PDB/1PDB.modif.pdb (protein, water, ions) ./data/1PDB/1PDB.ligand.pdb (ligand)
./data/1PDB/1PDB.log.tmp (disulfid bridges, alternative conformations,
sulfate, citrate)
./data/1PDB/1PDB.pml (pymol
script)
select
alternative conformations and delete not used residues
specify charge of ligand
xleap.sh
combine 1PDB.modif.pdb and
1PDB.ligand.pdb, add optional hydrogens with InsightII and/or WHATIF
and run molecular mechanic minimization
required programs: renumb babel (optional, for adding hydrogens, not really useful)
InsightII (optional, for adding hydrogens to ligand) pdbconv-insight (optional, for adding
hydrogens to ligand with
InsightII)
WHATIF (optional, for adding hydrogens to protein and water molecules) pdbconv-whatif2amber (optional,
for adding hydrogens with WHATIF-HBONDS (this option is not working at
the moment)) pdbconv-whatif2amber-new
(optional, for adding hydrogens with WHATIF-PROTON (default))
AMBER8
antechamber
parmchk
tleap cyxbond
sander
ambpdb
input:
./data/1PDB/1PDB.ALT.modif.pdb (protein, water, ions, without
alternative conformations)
./data/1PDB/1PDB.ligand.pdb
(ligand)
protmin.restrain.template (template for sander input)
leaprc.ff03
./Parameter/gaff.dat
./Parameter/added_ligand.parm
(optional, tleap parameter, important for
some ligands)
./Parameter/extra.parm (optional, tleap parameter)
./Parameter/extra.prep (optional, tleap parameter)
./Parameter/extra.lib
(optional, tleap parameter, eg. calcium ion)
output: ./data/1PDB/1PDB.ALT.modifnew.pdb (protein, ligand, water, ions)
./data/1PDB/1PDB.ligand.pdb
(ligand)
./data/1PDB/1PDB.ALT.xleap.script (script for second tleap run)
./data/1PDB/1PDB.ALT.top (final topology)
./data/1PDB/1PDB.ALT.cor (final
coordinates)
./data/1PDB/1PDB.prep (topology
of ligand)
./data/1PDB/1PDB.parm
(additional parameters for ligand) ./data/1PDB/1PDB.ALT.min.xyz
(minimized coordinates, sander output) ./data/1PDB/1PDB.ALT.min.pdb
(minimized coordinates, pdb format)
./data/1PDB/1PDB.ALT.tleap.log
(tleap logfile)
./data/1PDB/1PDB.ALT.min.out
(sander logfile)
1PDB.ALT.protmin.restrain.in
(sander input) some
temp-files, which are moved to ./data/1PDB/TMP.1PDB.ALT/
change to new directory for COMBINE analysis
current directory: ./combine/
prep_interaction.sh
collect all *.min.pdb files of
subdirectories in ./data/
input:
./combine/1PDB/1PDB.ALT.min.pdb (all minimized pdb files, with same
sequence length)
leaprc.ff03
./Parameter/gaff.dat
./Parameter/added_ligand.parm (optional, tleap parameter, important for
some ligands)
./Parameter/extra.parm (optional, tleap parameter)
./Parameter/extra.prep (optional, tleap parameter)
./Parameter/extra.lib (optional, tleap parameter, eg. calcium ion)
./data/1PDB/1PDB.prep (topology
of ligand)
./data/1PDB/1PDB.parm
(additional parameters for ligand)
output: ./combine/1PDB/1PDB.ALT.xcut.pdb (protein, ligand, ions)
./combine/1PDB/1PDB.ALT.aout (analyse output) ./combine/1PDB/1PDB_### (link to
./combine/1PDB/1PDB.ALT.aout)
interaction.log (output with path for used directories, names of pdb
structures)
activity.txt (template file for reading activity values in GOLPE)
dat.VarNames (file with variable names for GOLPE)
start GOLPE
4.5 and read ./combine/1PDB/1PDB_### create
GOLPE.dat file rename
dat.VarNames into GOLPE.dat.VarNames write
activity values in activity.txt and read it as Y-variables
make PCA and PLS analyses
pdbconv
source code: pdbconv.c compilation: cc -o pdbconv pdbconv.c
usage: pdbconv protein.pdb protein.modif.pdb
protein.ligand.pdb protein.log ligandname discription:
pdbconv is for converting pdb-files (eg. 1o3g.pdb) into amber-format by
using all given hydrogens, water molecules, ions and ligans. The
original
pdb-file protein.pdb is read in for each separate line. The
given
hydrogens (eg. 1HB in ALA) and ions (CA2+, CL) are renamed (eg. HB1,
CAA,
Cl-). According to the disulfid bonds marked in the header or the
protonation
state of HIS and ASP the residues are renamed into CYX, HID, HIE, HIP,
ASP
or ASH, respectively. The modified lines are written into
protein.modif.pdb.
Hydrogen, nitrogen and carbon atoms of the ligand (and other
heteroatoms
than calcium and chloride) are written into protein.ligand.pdb
with
the three letters of ligandname. Disulfide bonds, atoms with
alternative
conformations, calcium and chloride are written into
protein.log.
cyxbond
source code:cyxbond.c
compilation: cc -o cyxbond cyxbond.c
usage: cyxbond protein.modif.pdb protein.xleap.pdb
protein.cyxbond.out pdb-code discription:
cyxbond writes a script for the disulfide bridges using in an
amber-script. protein.modif.pdb is the modified pdb-file of
pdbconv with disulfide bridges marked in the header and renamed CYS
into CYX. According to the renumbering of residues in amber, which is
given byprotein.xleap.pdb, the script
protein.cyxbond.out is generated. In xleap.sh this script is
attached to other parts of amber-scripts. pdb-code is the
intern name
in the complete amber-script.
convert.sh
source code: bash-script usage:convert.sh discription: NEW: starting from command line
now possible!
concert.sh runs the program pdbconv. The in
normal cases only the pdb-code ($pdb) and the ligandname ($ligandname)
must be changed. The pdb-file must be in the current directory. A
script for running pymol is generated ($pdb.pml), which loads the
pdb-file and the electron density maps (save maps in ccp4-format in
scratch-directory before).
xleap.sh
source code: bash-script usage:xleap.sh discription: NEW: starting from command line
now possible!
With xleap.sh antechamber, parmchk, tleap, sander and ambpdb are
started, so the required environment setting for amber8 must be set
before (in EML: prepare amber8). The files protein.modif.pdb
and protein.ligand.pdb are in the specified directory
($directory). In most cases only the four-letter pdb-code, the
three-letter ligandname as given in protein.ligand.pdb and the
net charge of the ligand have to be changed.
The logfile of pdbconv (if it was set to
$pdb".log.tmp") is renamed into $pdb"log". Nealy all temp-files of
antechamber, amber and sander are moved into a new directory (TMP...).
With setting the variable $alt (eg. ".217A") several alternative
conformations can be handled by using the same
protein.ligand.pdb but different
protein.modif.pdb-files (eg. 1o3g.217A.modif.pdb,
1o3g.217B.modif.pdb,...). The protein.modif.pdb must be edited
by hand and saved under a new name.
For creating the amber-script the program cyxbond
must in the specified directory for programs ($prgdir).
The template-script (protmin.restrain.in)
and the program makemin are required
(directory $minimize) for generating minimization-script
(protmin.restrain.in) for sander.
(not used anymore) source code:makemin.c
compilation: cc -o makemin makemin.c
usage: makemin protmin.restrain.template
protmin.restrain.in
residue number of ligand first residue number of
protein last residue numer of protein discription:
In the template protmin.restrain.template
the residue numbers are given by $ligand, $start and $end, and will be
replaced by the specified numbers.
calcg.c
source code:calcg.C
compilation: g++ -o calcg calcg.C discription:
Calculate deltaG from Ki (in uM at temperature 298.15 K).
SDF-toolkit
extract_prop_sdf -property_name [ID | residue | uPA | PDB_uPA |...]
input.sdf extract the values with -property_name