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 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 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
-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 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 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 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 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/>.