Ubuntu Manpage: pdb2gmx - converts coordinate files to topology and FF-compliant coordinate files

Provided by: gromacs-data_4.6.5-1build1_all

NAME

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

       VERSION 4.6.5

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 -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

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 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
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
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
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. 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 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

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

       -[no]ssno
        Interactive SS bridge selection

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

       -[no]lysno
        Interactive lysine selection, instead of charged

       -[no]argno
        Interactive arginine selection, instead of charged

       -[no]aspno
        Interactive aspartic acid selection, instead of charged

       -[no]gluno
        Interactive glutamic acid selection, instead of charged

       -[no]glnno
        Interactive glutamine selection, instead of neutral

       -[no]hisno
        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]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

NAME

SYNOPSIS

DESCRIPTION

FILES

OTHER OPTIONS

SEE ALSO