gmx-pdb2gmx(1) GROMACS Manual gmx-pdb2gmx(1)NAMEgmx-pdb2gmx - Convert coordinate files to topology and FF-compliant
coordinate files
SYNOPSIS
gmx pdb2gmx [-f [<.gro/.g96/...>]] [-o [<.gro/.g96/...>]]
[-p [<.top>]] [-i [<.itp>]] [-n [<.ndx>]]
[-q [<.gro/.g96/...>]] [-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
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 force‐
field.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 cor‐
responding 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" respec‐
tively 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 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 han‐
dle this, gmx pdb2gmx uses two separate options. First, -chainsep
allows you to choose when a new chemical chain should start, and ter‐
mini 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 interac‐
tively.
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 ver‐
ify the correctness of the input data (read the article!).
During processing the atoms will be reordered according to GROMACS con‐
ventions. 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. There‐
fore 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 rela‐
tive 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.
OPTIONS
Options to specify input and output files:
-f [<.gro/.g96/...>] (eiwit.pdb) (Input)
Structure file: gro g96 pdb brk ent esp tpr tpb tpa
-o [<.gro/.g96/...>] (conf.gro) (Output)
Structure file: gro g96 pdb brk ent esp
-p [<.top>] (topol.top) (Output)
Topology file
-i [<.itp>] (posre.itp) (Output)
Include file for topology
-n [<.ndx>] (clean.ndx) (Output, Optional)
Index file
-q [<.gro/.g96/...>] (clean.pdb) (Output, Optional)
Structure file: gro g96 pdb brk ent esp
Other options:
-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, interactive
-merge <enum> (no)
Merge multiple chains into a single [moleculetype]: no, all, inter‐
active
-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
-[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 neutral
-[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, tryp‐
tophane and tyrosine
-[no]ignh (no)
Ignore hydrogen atoms that are in the coordinate file
-[no]missing (no)
Continue when atoms are missing, 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
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-pdb2gmx(1)
