programs

Programs for converting pdb-files into amber-format

convert.sh
xleap.sh
local_start.sh
local_sxleap.sh
gold_analysis.sh
prep_interaction.sh
calc_interaction.sh
calc_inter_model.sh

pdbconv
pdbconv-insight
pdbconv-whatif
pdbconv-whatif2amber
pdbconv-whatif2amber-new
renumb.C
cyx-distance.c
cut_sequence.c
calcg.c
grapsdtag

SDF-toolkit

add path to program directories

.bashrc_user
export PATH="/sw/mcm/app/prepare/:/sw/pub/bin/:/usr/lib:/sw/:/usr/local/bin:/sw/:/home/henricsn/Combine/tassfun/programs:./:$PATH"source /sw/mcm/app/prepare/prepare.bash

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/

required programs:
-

input:
./combine/1PDB/1PDB.ALT.min.pdb (all minimized pdb files)

output:
./combine/1PDB/1PDB.ALT.pdb.cut (protein, ligand, ions)

create an alignment (eg. with STRAP (STRAP))
cut all the pdb files *.pdb.cut to the same sequence length

calc_interaction.sh

run analyse modul of AMBER7 for calculating van de Waals and electrostatic interactions

required programs:
tleap AMBER8
anal AMBER7
renumb
cyxbond (optional)

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.

prep_interaction.sh

source code: bash-script
usage: prep_interaction.sh
discription:
Prepares minimized pdb-files with tleap of AMBER8 for calc_interaction.sh

calc_interaction.sh

source code: bash-script
usage: calc_interaction.sh
discription:
Calculates van de Waals and electrostatic interactions with analyse modul of AMBER7.

pdbconv-insight

source code: pdbconv-insight.c
compilation: cc -o pdbconv-insight pdbconv-insight.c
usage: pdbconv-insight protein.pdb protein.modif.pdb protein.hetatm.pdb ligandname
discription:
Converts ligand pdb file created in insightII into AMBER format.

pdbconv-whatif

source code: pdbconv-whatif.c
compilation: cc -o pdbconv-whatif pdbconv-whatif.c
usage: pdbconv-whatif protein.pdb protein.modif.pdb protein.hetatm.pdb ligandname
discription:
Converts ligand pdb file created in WHATIF into AMBER format.

pdbconv-whatif2amber

source code: pdbconv-whatif2amber.c
compilation: cc -o pdbconv-whatif2amber pdbconv-whatif2amber.c
usage: pdbconv whatifout.pdb whatif2amber.pdb ligandname
discription:
Converts of WHATIF output pdb files (generated with HBONDS command, not working) for AMBER.

pdbconv-whatif2amber-new

source code: pdbconv-whatif2amber-new.c
compilation: cc -o pdbconv-whatif2amber pdbconv-whatif2amber.c
usage: pdbconv whatifout.pdb whatif2amber.pdb ligandname
discription:
Converts of WHATIF output pdb files (generated with PROTON command, default) for AMBER.

renumb

source code: renumb.c
compilation: g++ -o renumb renumb.C
usage: renumb protein.modif.pdb protein.renumb.pdb
discription:
Renumbers residue of pdb files.

makemin.c

(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

update: 13.09.05