Provided by: gromacs-data_2019.1-1_all bug


       gmx-pdb2gmx - Convert coordinate files to topology and FF-compliant coordinate files


          gmx pdb2gmx [-f [<.gro/.g96/...>]] [-o [<.gro/.g96/...>]] [-p [<.top>]]
                      [-i [<.itp>]] [-n [<.ndx>]] [-q [<.gro/.g96/...>]]
                      [-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]


       gmx  pdb2gmx 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.

       gmx 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  gmx  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,  gmx
       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

       gmx 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 file.

       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 (but this feature is deprecated).  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 atoms.

       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.


       Options to specify input files:

       -f [<.gro/.g96/…>] (protein.pdb)
              Structure file: gro g96 pdb brk ent esp tpr

       Options to specify output files:

       -o [<.gro/.g96/…>] (conf.gro)
              Structure file: gro g96 pdb brk ent esp

       -p [<.top>] (
              Topology file

       -i [<.itp>] (posre.itp)
              Include file for topology

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       -q [<.gro/.g96/…>] (clean.pdb) (Optional)
              Structure file: gro g96 pdb brk ent esp

       Other options:

       -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, interactive

       -merge <enum> (no)
              Merge multiple chains into a single [moleculetype]: no, all, 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, tip5p, tips3p

       -[no]inter (no)
              Set the next 8 options to interactive

       -[no]ss (no)
              Interactive SS bridge selection

       -[no]ter (no)
              Interactive termini selection, instead of charged (default)

       -[no]lys (no)
              Interactive lysine selection, instead of charged

       -[no]arg (no)
              Interactive arginine selection, instead of charged

       -[no]asp (no)
              Interactive aspartic acid selection, instead of charged

       -[no]glu (no)
              Interactive glutamic acid selection, instead of charged

       -[no]gln (no)
              Interactive glutamine selection, instead of charged

       -[no]his (no)
              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)

       -[no]una (no)
              Select aromatic rings with  united  CH  atoms  on  phenylalanine,  tryptophane  and

       -[no]ignh (no)
              Ignore hydrogen atoms that are in the coordinate file

       -[no]missing (no)
              Continue when atoms are missing and bonds cannot be made, dangerous

       -[no]v (no)
              Be slightly more verbose in messages

       -posrefc <real> (1000)
              Force constant for position restraints

       -vsite <enum> (none)
              Convert atoms to virtual sites: none, hydrogens, aromatics

       -[no]heavyh (no)
              Make hydrogen atoms heavy

       -[no]deuterate (no)
              Change the mass of hydrogens to 2 amu

       -[no]chargegrp (yes)
              Use charge groups in the .rtp file

       -[no]cmap (yes)
              Use cmap torsions (if enabled in the .rtp file)

       -[no]renum (no)
              Renumber the residues consecutively in the output

       -[no]rtpres (no)
              Use .rtp entry names as residue names



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       2019, GROMACS development team