NAME
pdb2gmx - converts pdb files to topology and coordinate files
VERSION 4.0.1
SYNOPSIS
pdb2gmx -f eiwit.pdb -o conf.gro -p topol.top -i posre.itp -n clean.ndx
-q clean.pdb -[no]h -nice int -[no]merge -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
DESCRIPTION
This program reads a pdb file, reads some database files, adds
hydrogens to the molecules and generates coordinates in Gromacs
(Gromos) format and a topology in Gromacs format. These files can
subsequently be processed to generate a run input file.
The force fields in the distribution are currently:
oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
G43b1 GROMOS96 43b1 Vacuum Forcefield
G43a1 GROMOS96 43a1 Forcefield
G43a2 GROMOS96 43a2 Forcefield (improved alkane dihedrals)
G45a3 GROMOS96 45a3 Forcefield
G53a5 GROMOS96 53a5 Forcefield
G53a6 GROMOS96 53a6 Forcefield
gmx Gromacs Forcefield (a modified GROMOS87, see manual)
encads Encad all-atom force field, using scaled-down vacuum charges
encadv Encad all-atom force field, using full solvent charges
The corresponding data files can be found in the library directory with
names like ffXXXX.YYY. Check chapter 5 of the manual for more
information about file formats. By default the forcefield selection is
interactive, but you can use the -ff option to specify one of the
short names above on the command line instead. In that case pdb2gmx
just looks for the corresponding file.
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 LYS (two protons on NZ) or LYSH (three
protons, default), for ASP and GLU unprotonated (default) or
protonated, for HIS the proton can be either on ND1 (HISA), on NE2
(HISB) or on both (HISH). 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
criterium, specified by the maximum hydrogen-donor-acceptor angle and
donor-acceptor distance, which are set by -angle and -dist
respectively.
Option -merge will ask if you want to merge consecutive chains into
one molecule definition, this can be useful for connecting chains with
a disulfide brigde or intermolecular distance restraints.
pdb2gmx will also check the occupancy field of the pdb file. If any of
the occupanccies 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 multichain 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, elminating 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 tpb tpa
-o conf.gro Output
Structure file: gro g96 pdb
-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
OTHER OPTIONS
-[no]hno
Print help info and quit
-nice int 0
Set the nicelevel
-[no]mergeno
Merge chains into one molecule definition
-ff string select
Force field, interactive by default. Use -h for information.
-water enum spc
Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P:
spc, spce, tip3p, tip4p, tip5p or f3c
-[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 Arganine 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 pdb 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
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 pdb2gmx(1)