Provided by: gromacs-data_4.6.5-1build1_all bug


       pdb2gmx - converts coordinate files to topology and FF-compliant coordinate files

       VERSION 4.6.5


       pdb2gmx  -f  eiwit.pdb  -o  conf.gro  -p -i posre.itp -n clean.ndx -q clean.pdb
       -[no]h -[no]version -nice int -chainsep enum -merge enum -ff string -water enum -[no]inter
       -[no]ss  -[no]ter  -[no]lys -[no]arg -[no]asp -[no]glu -[no]gln -[no]his -angle real -dist
       real  -[no]una  -[no]ignh  -[no]missing  -[no]v  -posrefc  real  -vsite  enum  -[no]heavyh
       -[no]deuterate -[no]chargegrp -[no]cmap -[no]renum -[no]rtpres


       This  program  reads a  .pdb (or  .gro) file, reads some database files, adds hydrogens to
       the molecules and generates coordinates in GROMACS (GROMOS), or optionally   .pdb,  format
       and a topology in GROMACS format.  These files can subsequently be processed to generate a
       run input file.

        pdb2gmx  will  search  for  force  fields  by  looking  for  a   forcefield.itp  file  in
       subdirectories   forcefield.ff of the current working directory and of the GROMACS library
       directory as inferred from the path of the binary or the  GMXLIB environment variable.  By
       default  the  forcefield  selection  is  interactive,  but  you can use the  -ff option to
       specify one of the short names in the list on the  command  line  instead.  In  that  case
       pdb2gmx just looks for the corresponding  forcefield.ff 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   residuetypes.dat  in
       the library directory or copy the whole library directory to a local directory and set the
       environment variable  GMXLIB to the name of that directory.  Check Chapter 5 of the manual
       for more information about file formats.

       Note  that  a   .pdb  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

       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
       is desired. 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  -angle  and
       -dist respectively.

       The protonation state of N- and C-termini can be chosen interactively with the  -ter flag.
       Default termini are ionized (NH3+ and COO-),  respectively.   Some  force  fields  support
       zwitterionic  forms  for  chains of one residue, but for polypeptides these options should
       NOT be selected.  The AMBER force fields have unique forms for the terminal residues,  and
       these  are incompatible with the  -ter mechanism. You need to prefix your N- or C-terminal
       residue names with "N" or "C" respectively to use these forms, making  sure  you  preserve
       the  format  of  the  coordinate file. Alternatively, use named terminating residues (e.g.
       ACE, NME).

       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  moleculetype definition.  To handle this,  pdb2gmx
       uses  two  separate  options.   First,  -chainsep allows you to choose when a new chemical
       chain should start, and termini added when applicable. This  can  be  done  based  on  the
       existence  of TER records, when the chain id changes, or combinations of either or both of
       these. You can also do the selection fully interactively.  In addition, there is a  -merge
       option  that  controls  how multiple chains are merged into one moleculetype, after adding
       all the chemical termini (or not).  This can be turned off  (no  merging),  all  non-water
       chains can be merged into a single molecule, or the selection can be done interactively.

        pdb2gmx will also check the occupancy field of the  .pdb file.  If any of the occupancies
       are not one, indicating that the atom is not resolved well in  the  structure,  a  warning
       message  is  issued.   When  a   .pdb  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  -n
       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  -ignh.

       The   .gro and  .g96 file formats do not support chain identifiers. Therefore it is useful
       to enter a  .pdb file name at the  -o option when you want to convert a multi-chain   .pdb

       The  option   -vsite  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.  Note 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

       Also slowing down of dihedral motion can be done with   -heavyh  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.


       -f eiwit.pdb Input
        Structure file: gro g96 pdb tpr etc.

       -o conf.gro Output
        Structure file: gro g96 pdb etc.

       -p Output
        Topology file

       -i posre.itp Output
        Include file for topology

       -n clean.ndx Output, Opt.
        Index file

       -q clean.pdb Output, Opt.
        Structure file: gro g96 pdb etc.


        Print help info and quit

        Print version info and quit

       -nice int 0
        Set the nicelevel

       -chainsep enum id_or_ter
        Condition  in  PDB files when a new chain should be started (adding termini):  id_or_ter,
       id_and_ter,  ter,  id or  interactive

       -merge enum no
        Merge multiple chains into a single [moleculetype]:  no,  all or  interactive

       -ff string select
        Force field, interactive by default. Use  -h for information.

       -water enum select
        Water model to use:  select,  none,  spc,  spce,  tip3p,  tip4p or  tip5p

        Set the next 8 options to interactive

        Interactive SS bridge selection

        Interactive termini selection, instead of charged (default)

        Interactive lysine selection, instead of charged

        Interactive arginine selection, instead of charged

        Interactive aspartic acid selection, instead of charged

        Interactive glutamic acid selection, instead of charged

        Interactive glutamine selection, instead of neutral

        Interactive histidine selection, instead of checking H-bonds

       -angle real 135
        Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)

       -dist real 0.3
        Maximum donor-acceptor distance for a H-bond (nm)

        Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine

        Ignore hydrogen atoms that are in the coordinate file

        Continue when atoms are missing, dangerous

        Be slightly more verbose in messages

       -posrefc real 1000
        Force constant for position restraints

       -vsite enum none
        Convert atoms to virtual sites:  none,  hydrogens or  aromatics

        Make hydrogen atoms heavy

        Change the mass of hydrogens to 2 amu

        Use charge groups in the  .rtp file

        Use cmap torsions (if enabled in the  .rtp file)

        Renumber the residues consecutively in the output

        Use  .rtp entry names as residue names



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               pdb2gmx(1)