Using the MMTSB Tool Set

Using the MMTSB Tool Set MMTSB NIH Research Resource PSC Workshop 2003

Architecture of MMTSB Tool Set

MMTSB Tool Set Package o Available from: (free for academic use) http://mmtsb.scripps.edu/software/mmtsbtoolset.html o Includes: Perl packages (.pm) Perl utilities (.pl) External programs (MONSSTER, rebuild, etc.) o Needs: Perl Version 5.004 or newer Compilers (FORTRAN 77, C++)

Supported Platforms o Linux (PC, Alpha) o SGI Irix o DEC OSF/1 o IBM AIX o Sun Solaris o MacOS X o UNIX + Perl + GNU compilers o Windows?

Package Installation o Download Tool Set Package (Register!) o Unpack > cd /usr/local/mmtsb > gunzip mmtsb.tar.gz > tar xvf mmtsb.tar o Run install.sh >./install.sh o Set environment setenv MMTSBDIR /usr/local/mmtsb set path = ( $path $MMTSBDIR/perl $MMTSBDIR/bin )

External Programs: CHARMM/Amber o CHARMM (c29b, c30a, or newer) http://www.scripps.edu/brooks/charmm_docs/charmm.html setenv CHARMMEXEC /usr/local/bin/charmm.exe setenv CHARMMDATA /usr/local/data/charmm o Amber (Version 7) http://www.amber.ucsf.edu/amber/ setenv AMBERHOME /usr/local/amber7 setenv SANDEREXEC /usr/local/bin/sander.exe

Other External Programs o SCWRL Version 2.95 (Dunbrack) http://www.fccc.edu/research/labs/dunbrack/scwrl/ > cp scwrl $MMTSBDIR/bin o DSSP (Kabsch & Sander) http://www.cmbi.kun.nl/gv/dssp/ > cp dsspcmbi $MMTSBDIR/bin

Using the MMTSB Tool Set Command-line oriented utilities > mincharmm.pl 1vii.pdb with options: > mincharmm.pl par minsteps=100,nocut 1vii.pdb Use MMTSB Packages in new Perl scripts #!/usr/bin/perl use Molecule; my $mol = &Molecule::new(); $mol->readpdb( 1vii.pdb );

Input / Output Input usually expected from file name or std input > mincharmm.pl 1vii.pdb > cat 1vii.pdb mincharmm.pl Output usually written to standard output > mincharmm.pl 1vii.pdb > 1vii.min.pdb - can be used for standard input/output > cat 1vii.pdb lsqfit.pl 1vii.min.pdb > mincharmm.pl log 1vii.pdb Command pipes > mincharmm.pl 1vii.pdb mdcharmm.pl

All Atom Structure Representation: PDB Formats PDB CHARMM22 CHARMM19 Amber ILE Cd CD1 CD CD CD1 HIS prot Nd HIS HSD HIS HID HIS prot Ne HIS HSE HSD HIE N-terminus 1H/2H/3H HT1/HT2/HT3 HT1/HT2/HT3 H1/H2/H3 C-terminus O/OXT OT1/OT2 OT1/OT2 O/OXT Hydrogens 1HB/2HB HB1/HB2 - HB2/HB3 CYS S-S CYS CYS CYS CYX

All Atom Structure Representation: Multiple Chains, Ligands Multiple chains Chain IDs are used to separate chains CHARMM segment IDs are generated automatically HETATM records (solvent, ligands, cofactors) Read into single chain (+) but written out as HETATM Explicit solvent Recognized if residue name TIP3/OH2 and ATOM rec. Disulfides SSBOND entry recognized and kept

Parallel Execution Parallelism within CHARMM/Amber: parallel molecular dynamics / minimization tightly coupled, based on MPI setenv CHARMMEXEC mpirun n 8 /usr/local/bin/charmm.exe setenv SANDEREXEC mpirun n 8 /usr/local/bin/sander.exe Parallelism within MMTSB Tool Set ensemble computing, replica exchange simulations TCP/IP socket-based server/client architecture

MMTSB Parallel Options: Shared Memory Server Client 1 Client 2 Client 3 > ensrun.pl cpus 4 > aarex.pl temp 4:300:350 use 4 CPUs for 4 clients + server on SMP architecture Client 4

MMTSB Parallel Options: Distributed Environment Node 1 Node 2 Server Client 1 Client 2 Client 3 > ensrun.pl cpus 4 hosts hlist > ensrun.pl cpus 4 mp hosts hlist Host file: node1 1 /tmp/mmtsb node2 2 /tmp/mmtsb node3 1 /tmp/mmtsb Node 3 Client 4 uses 4 CPUs on 3 nodes requires rsh to work with.rhosts

MMTSB Parallel Options: PSC Environment Jobs are placed on each node with prun Environment variable RMS_RANK contains rank for more than one node: > prun N all ensrun.pl jobenv RMS_RANK saveid id.file node 0 starts server and writes id.file all nodes wait for id.file and connect as clients

-help option Help/Documentation > dihed.pl help usage: dihed.pl [options] [refpdb [cmppdb]] options: [-l min:max[...]] [-list phi psi chi1 omega] Online manual pages with examples http://mmtsb.scripps.edu/cgi-bin/tooldoc Tutorials (in progress) http://mmtsb.scripps.edu/software/tutorial/protmodel.html Email support: mmtsb@scripps.edu Mailing List: available soon

Utility Functions PDB format and structure manipulation convpdb.pl complete.pl Structure analysis lsqfit.pl, rms.pl dihed.pl contacts.pl rgyr.pl genseq.pl -dssp

Conversion between PDB Formats convpdb.pl Generate specific PDB format > convpdb.pl out amber 1vii.pdb ATOM 1 N MET 1 1.177-10.035-3.493 1.00 0.00 ATOM 2 H1 MET 1 1.833-10.061-2.687 1.00 0.00 ATOM 3 H2 MET 1 1.719-9.981-4.379 1.00 0.00 ATOM 4 H3 MET 1 0.596-10.897-3.495 1.00 0.00 ATOM 5 CA MET 1 0.292-8.839-3.377 1.00 0.00 ATOM 6 HA MET 1 0.900-7.946-3.376 1.00 0.00 ATOM 7 CB MET 1-0.674-8.793-4.565 1.00 0.00 ATOM 8 HB2 MET 1-1.656-8.393-4.233 1.00 0.00 ATOM 9 HB3 MET 1-0.821-9.818-4.967 1.00 0.00 > convpdb.pl segnames out charmm22 1vii.pdb ATOM 1 N MET 1 1.177-10.035-3.493 1.00 0.00 PRO0 ATOM 2 HT1 MET 1 1.833-10.061-2.687 1.00 0.00 PRO0 ATOM 3 HT2 MET 1 1.719-9.981-4.379 1.00 0.00 PRO0 ATOM 4 HT3 MET 1 0.596-10.897-3.495 1.00 0.00 PRO0 ATOM 5 CA MET 1 0.292-8.839-3.377 1.00 0.00 PRO0

Manipulation of PDB Files convpdb.pl Renumber residues > convpdb.pl renumber 5 1vii.pdb ATOM 1 N MET 5 1.177-10.035-3.493 1.00 0.00 ATOM 2 HT1 MET 5 1.833-10.061-2.687 1.00 0.00 ATOM 3 HT2 MET 5 1.719-9.981-4.379 1.00 0.00 ATOM 4 HT3 MET 5 0.596-10.897-3.495 1.00 0.00 ATOM 5 CA MET 5 0.292-8.839-3.377 1.00 0.00 Center structure at coordinate origin > convpdb.pl center 1vii.pdb ATOM 1 N MET 1 0.437-10.341-5.602 1.00 0.00 ATOM 2 HT1 MET 1 1.093-10.367-4.796 1.00 0.00 ATOM 3 HT2 MET 1 0.979-10.287-6.488 1.00 0.00 ATOM 4 HT3 MET 1-0.144-11.203-5.604 1.00 0.00 ATOM 5 CA MET 1-0.448-9.145-5.486 1.00 0.00

Subselection from PDB Files convpdb.pl Residue subset by number > convpdb.pl sel 10:15 1vii.pdb ATOM 141 N VAL 10-1.787-4.543 8.123 1.00 0.00 ATOM 142 HN VAL 10-2.629-4.094 7.835 1.00 0.00 ATOM 143 CA VAL 10-0.514-3.998 7.587 1.00 0.00 Residue subset by sequence > convpdb.pl selseq VFGMT 1vii.pdb ATOM 141 N VAL 10-1.787-4.543 8.123 1.00 0.00 ATOM 142 HN VAL 10-2.629-4.094 7.835 1.00 0.00 ATOM 143 CA VAL 10-0.514-3.998 7.587 1.00 0.00 NMR model selection > convpdb.pl model 2 1d3z.pdb ATOM 1 N MET A 1 54.015-88.009 9.498 1.00 9.67 ATOM 2 CA MET A 1 52.647-87.443 9.674 1.00 10.38 ATOM 3 C MET A 1 51.877-87.557 8.364 1.00 9.62

Completing All-atom Structures: complete.pl > complete.pl model.pdb ATOM 1 N MET 1 0.774-7.875-4.381 1.00 0.00 ATOM 2 HT1 MET 1-0.029-7.328-4.751 1.00 0.00 ATOM 3 HT2 MET 1 1.233-8.387-5.161 1.00 0.00 ATOM 4 HT3 MET 1 1.460-7.229-3.940 1.00 0.00 ATOM 5 CA MET 1 0.292-8.839-3.377 1.00 0.00 Ca Rebuild backbone Ca sufficient, but rebuilds only what is missing Add side chains Add hydrogen atoms

Superposition of Structures lsqfit.pl Superposition of entire structure > lsqfit.pl 1vii.pdb 1vii.sample.pdb Superposition of subset > lsqfit.pl l 10:15 1vii.pdb 1vii.sample.pdb > lsqfit.pl x 10:15 1vii.pdb 1vii.sample.pdb Superposition with different sequence > lsqfit.pl resnumonly l 10:15 1vii.pdb helix.pdb

Comparison of Different Conformations rms.pl Coordinate RMSD with respect to reference > rms.pl out CA fit 1vii.pdb 1vii.sample.pdb 2.6944 CA > rms.pl l 10:15 fitxl 1vii.pdb 1vii.sample.pdb > rms.pl fitl 10:15 1vii.pdb 1vii.sample.pdb Other possible values: CA, CB, CAB, heavy, all,

Peptide Dihedral Angles: dihed.pl Calculate f/y/w/c 1 dihedral angles > dihed.pl list phi,psi,omega,chi1 1vii.pdb MET1: 0.000 132.907-179.006-95.176 LEU2: -64.308 100.191 178.918-106.206 SER3: -63.139 154.230-179.441 21.582 Calculate dihedral RMSD > dihed.pl 1vii.pdb 1vii.sample.pdb phi: 29.556 ( 88.57 % ), psi: 43.898 ( 80.00 % ), chi1: 61.341 ( 45.16 % ) c 1

Side Chain Contacts: contact.pl List side chain contacts (min. distance < 4.2 Å) > contact.pl list 1vii.pdb 2 7 3.525115 2 10 3.383307 2 11 3.541492 2 15 2.839893 2 34 2.930046 Compare contacts to reference > contact.pl 1vii.pdb 1vii.sample.pdb 15 contacts ( fraction: 0.625000 ), rho: 0.634847

Radius of Gyration: rgyr.pl > rgyr.pl 1vii.pdb 9.389212 > rgyr.pl caonly 1vii.pdb 8.817567 1 c = N r g  i 1 = N r  i i (r i - 2 c)

Secondary Structure Analysis: genseq.pl -dssp > genseq.pl out onesec -dssp 1vii.pdb MLSDEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLF UUUHHHHHUUUUUUHHHHUUUUHHHHHHHHHHUUUU Secondary structure identified from hydrogen bonding: H helical (a) E extended (b) U random coil/undefined