pdb2gmx(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					pdb2gmx(1)

NAME

       pdb2gmx - converts pdb files to topology and coordinate files

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       pdb2gmx	-f  eiwit.pdb  -o  conf.gro  -p  topol.top -i posre.itp -n clean.ndx -q clean.pdb -[no]h -[no]version -nice int -chainsep 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

DESCRIPTION

       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 direc-
       tory 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 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, spec-
       ified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by  -angle and  -dist respectively.

       The separation of chains is not entirely trivial since the markup in user-generated PDB files frequently varies and sometimes it is  desir-
       able 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 has an option  -chainsep 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.

	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  hydro-
       gens  into  virtual  sites and fixing angles, which fixes their position relative to neighboring atoms. Additionally, all atoms in the aro-
       matic 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 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.

FILES

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

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

       -p topol.top 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.

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	Set the nicelevel

       -chainsep enum id_or_ter
	Condition in PDB files when a new chain and molecule_type should be started:  id_or_ter,  id_and_ter,  ter,  id 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

       -[no]interno
	Set the next 8 options to interactive

       -[no]ssno
	Interactive SS bridge selection

       -[no]terno
	Interactive termini selection, iso charged

       -[no]lysno
	Interactive lysine selection, iso charged

       -[no]argno
	Interactive arginine selection, iso charged

       -[no]aspno
	Interactive aspartic Acid selection, iso charged

       -[no]gluno
	Interactive glutamic Acid selection, iso charged

       -[no]glnno
	Interactive glutamine selection, iso neutral

       -[no]hisno
	Interactive histidine selection, iso 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]unano
	Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine

       -[no]ignhno
	Ignore hydrogen atoms that are in the coordinate file

       -[no]missingno
	Continue when atoms are missing, dangerous

       -[no]vno
	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

       -[no]heavyhno
	Make hydrogen atoms heavy

       -[no]deuterateno
	Change the mass of hydrogens to 2 amu

       -[no]chargegrpyes
	Use charge groups in the  .rtp file

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

       -[no]renumno
	Renumber the residues consecutively in the output

       -[no]rtpresno
	Use  .rtp entry names as residue names

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							pdb2gmx(1)