Provided by: gromacs-data_2024.2-1_all 
NAME
gmx-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/...>]]
[-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 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 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, 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 interactively.
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. As a special case, ring-closed (or cyclic) molecules are considered. gmx
pdb2gmx automatically determines if a cyclic molecule is present by evaluating the distance between the
terminal atoms of a given chain. If this distance is greater than the -sb ("Short bond warning
distance", default 0.05 nm) and less than the -lb ("Long bond warning distance", default 0.25 nm) the
molecule is considered to be ring closed and will be processed as such. Please note that this does not
detect cyclic bonds over periodic boundaries.
OPTIONS
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>] (topol.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 tyrosine
-[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
SEE ALSO
gmx(1)
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2024, GROMACS development team
2024.2 May 10, 2024 GMX-PDB2GMX(1)