.TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c" .SH NAME pdb2gmx - converts pdb files to topology and coordinate files .B VERSION 4.5.4-dev-20110404-bc5695c .SH SYNOPSIS \f3pdb2gmx\fP .BI "\-f" " eiwit.pdb " .BI "\-o" " conf.gro " .BI "\-p" " topol.top " .BI "\-i" " posre.itp " .BI "\-n" " clean.ndx " .BI "\-q" " clean.pdb " .BI "\-[no]h" "" .BI "\-[no]version" "" .BI "\-nice" " int " .BI "\-chainsep" " enum " .BI "\-ff" " string " .BI "\-water" " enum " .BI "\-[no]inter" "" .BI "\-[no]ss" "" .BI "\-[no]ter" "" .BI "\-[no]lys" "" .BI "\-[no]arg" "" .BI "\-[no]asp" "" .BI "\-[no]glu" "" .BI "\-[no]gln" "" .BI "\-[no]his" "" .BI "\-angle" " real " .BI "\-dist" " real " .BI "\-[no]una" "" .BI "\-[no]ignh" "" .BI "\-[no]missing" "" .BI "\-[no]v" "" .BI "\-posrefc" " real " .BI "\-vsite" " enum " .BI "\-[no]heavyh" "" .BI "\-[no]deuterate" "" .BI "\-[no]chargegrp" "" .BI "\-[no]cmap" "" .BI "\-[no]renum" "" .BI "\-[no]rtpres" "" .SH DESCRIPTION \&This program reads a \fB .pdb\fR (or \fB .gro\fR) file, reads \&some database files, adds hydrogens to the molecules and generates \&coordinates in GROMACS (GROMOS), or optionally \fB .pdb\fR, format \&and a topology in GROMACS format. \&These files can subsequently be processed to generate a run input file. \& \&\fB pdb2gmx\fR will search for force fields by looking for \&a \fB forcefield.itp\fR file in subdirectories \fB forcefield.ff\fR \&of the current working directory and of the Gromacs library directory \&as inferred from the path of the binary or the \fB GMXLIB\fR environment \&variable. \&By default the forcefield selection is interactive, \&but you can use the \fB \-ff\fR option to specify one of the short names \&in the list on the command line instead. In that case \fB pdb2gmx\fR just looks \&for the corresponding \fB forcefield.ff\fR directory. \& \&After choosing a force field, all files will be read only from \&the corresponding force field directory. \&If you want to modify or add a residue types, you can copy the force \&field directory from the Gromacs library directory to your current \&working directory. If you want to add new protein residue types, \&you will need to modify \fB residuetypes.dat\fR in the library directory \&or copy the whole library directory to a local directory and set \&the environment variable \fB GMXLIB\fR to the name of that directory. \&Check Chapter 5 of the manual for more information about file formats. \& \&Note that a \fB .pdb\fR file is nothing more than a file format, and it \&need not necessarily contain a protein structure. Every kind of \&molecule for which there is support in the database can be converted. \&If there is no support in the database, you can add it yourself. \&The program has limited intelligence, it reads a number of database \&files, that allow it to make special bonds (Cys\-Cys, Heme\-His, etc.), \&if necessary this can be done manually. The program can prompt the \&user to select which kind of LYS, ASP, GLU, CYS or HIS residue she \&wants. For LYS the choice is between neutral (two protons on NZ) or \&protonated (three protons, default), for ASP and GLU unprotonated \&(default) or protonated, for HIS the proton can be either on ND1, \&on NE2 or on both. By default these selections are done automatically. \&For His, this is based on an optimal hydrogen bonding \&conformation. Hydrogen bonds are defined based on a simple geometric \&criterion, specified by the maximum hydrogen\-donor\-acceptor angle \&and donor\-acceptor distance, which are set by \fB \-angle\fR and \&\fB \-dist\fR respectively. \&The separation of chains is not entirely trivial since the markup \&in user\-generated PDB files frequently varies and sometimes it \&is desirable to merge entries across a TER record, for instance \&if you want a disulfide bridge or distance restraints between \&two protein chains or if you have a HEME group bound to a protein. \&In such cases multiple chains should be contained in a single \&\fB moleculetype\fR definition. \&To handle this, \fB pdb2gmx\fR has an option \fB \-chainsep\fR so you can \&choose whether a new chain should start when we find a TER record, \&when the chain id changes, combinations of either or both of these \&or fully interactively. \&\fB pdb2gmx\fR will also check the occupancy field of the \fB .pdb\fR file. \&If any of the occupancies are not one, indicating that the atom is \¬ resolved well in the structure, a warning message is issued. \&When a \fB .pdb\fR file does not originate from an X\-ray structure determination \&all occupancy fields may be zero. Either way, it is up to the user \&to verify the correctness of the input data (read the article!). \&During processing the atoms will be reordered according to GROMACS \&conventions. With \fB \-n\fR an index file can be generated that \&contains one group reordered in the same way. This allows you to \&convert a GROMOS trajectory and coordinate file to GROMOS. There is \&one limitation: reordering is done after the hydrogens are stripped \&from the input and before new hydrogens are added. This means that \&you should not use \fB \-ignh\fR. \&The \fB .gro\fR and \fB .g96\fR file formats do not support chain \&identifiers. Therefore it is useful to enter a \fB .pdb\fR file name at \&the \fB \-o\fR option when you want to convert a multi\-chain \fB .pdb\fR file. \& \&The option \fB \-vsite\fR removes hydrogen and fast improper dihedral \&motions. Angular and out\-of\-plane motions can be removed by changing \&hydrogens into virtual sites and fixing angles, which fixes their \&position relative to neighboring atoms. Additionally, all atoms in the \&aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS) \&can be converted into virtual sites, eliminating the fast improper dihedral \&fluctuations in these rings. \fB Note\fR that in this case all other hydrogen \&atoms are also converted to virtual sites. The mass of all atoms that are \&converted into virtual sites, is added to the heavy atoms. \&Also slowing down of dihedral motion can be done with \fB \-heavyh\fR \&done by increasing the hydrogen\-mass by a factor of 4. This is also \&done for water hydrogens to slow down the rotational motion of water. \&The increase in mass of the hydrogens is subtracted from the bonded \&(heavy) atom so that the total mass of the system remains the same. .SH FILES .BI "\-f" " eiwit.pdb" .B Input Structure file: gro g96 pdb tpr etc. .BI "\-o" " conf.gro" .B Output Structure file: gro g96 pdb etc. .BI "\-p" " topol.top" .B Output Topology file .BI "\-i" " posre.itp" .B Output Include file for topology .BI "\-n" " clean.ndx" .B Output, Opt. Index file .BI "\-q" " clean.pdb" .B Output, Opt. Structure file: gro g96 pdb etc. .SH OTHER OPTIONS .BI "\-[no]h" "no " Print help info and quit .BI "\-[no]version" "no " Print version info and quit .BI "\-nice" " int" " 0" Set the nicelevel .BI "\-chainsep" " enum" " id_or_ter" Condition in PDB files when a new chain and molecule_type should be started: \fB id_or_ter\fR, \fB id_and_ter\fR, \fB ter\fR, \fB id\fR or \fB interactive\fR .BI "\-ff" " string" " select" Force field, interactive by default. Use \fB \-h\fR for information. .BI "\-water" " enum" " select" Water model to use: \fB select\fR, \fB none\fR, \fB spc\fR, \fB spce\fR, \fB tip3p\fR, \fB tip4p\fR or \fB tip5p\fR .BI "\-[no]inter" "no " Set the next 8 options to interactive .BI "\-[no]ss" "no " Interactive SS bridge selection .BI "\-[no]ter" "no " Interactive termini selection, iso charged .BI "\-[no]lys" "no " Interactive lysine selection, iso charged .BI "\-[no]arg" "no " Interactive arginine selection, iso charged .BI "\-[no]asp" "no " Interactive aspartic Acid selection, iso charged .BI "\-[no]glu" "no " Interactive glutamic Acid selection, iso charged .BI "\-[no]gln" "no " Interactive glutamine selection, iso neutral .BI "\-[no]his" "no " Interactive histidine selection, iso checking H\-bonds .BI "\-angle" " real" " 135 " Minimum hydrogen\-donor\-acceptor angle for a H\-bond (degrees) .BI "\-dist" " real" " 0.3 " Maximum donor\-acceptor distance for a H\-bond (nm) .BI "\-[no]una" "no " Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine .BI "\-[no]ignh" "no " Ignore hydrogen atoms that are in the coordinate file .BI "\-[no]missing" "no " Continue when atoms are missing, dangerous .BI "\-[no]v" "no " Be slightly more verbose in messages .BI "\-posrefc" " real" " 1000 " Force constant for position restraints .BI "\-vsite" " enum" " none" Convert atoms to virtual sites: \fB none\fR, \fB hydrogens\fR or \fB aromatics\fR .BI "\-[no]heavyh" "no " Make hydrogen atoms heavy .BI "\-[no]deuterate" "no " Change the mass of hydrogens to 2 amu .BI "\-[no]chargegrp" "yes " Use charge groups in the \fB .rtp\fR file .BI "\-[no]cmap" "yes " Use cmap torsions (if enabled in the \fB .rtp\fR file) .BI "\-[no]renum" "no " Renumber the residues consecutively in the output .BI "\-[no]rtpres" "no " Use \fB .rtp\fR entry names as residue names .SH SEE ALSO .BR gromacs(7) More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.