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gmx pdb2gmx [-f [<.gro/.g96/...>]] [-o [<.gro/.g96/...>]] [-p [<.top>]] [-i [<.itp>]] [-n [<.ndx>]] [-q [<.gro/.g96/...>]] [-nice
] [-chainsep ] [-merge ] [-ff ] [-water ] [-[no]inter] [-[no]ss] [-[no]ter] [-[no]lys] [-[no]arg] [-[no]asp] [-[no]glu] [-[no]gln] [-[no]his] [-angle ] [-dist ] [-[no]una] [-[no]ignh] [-[no]missing] [-[no]v] [-posrefc ] [-vsite ] [-[no]heavyh] [-[no]deuterate] [-[no]chargegrp] [-[no]cmap] [-[no]renum] [-[no]rtpres]
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. 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.