Provided by: gromacs-data_2023.1-2ubuntu1_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)
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2023, GROMACS development team