1pdb2gmx(1) GROMACS suite, VERSION 4.5 pdb2gmx(1)
2
6 pdb2gmx - converts pdb files to topology and coordinate files
7 VERSION 4.5
9
11 pdb2gmx -f eiwit.pdb -o conf.gro -p topol.top -i posre.itp -n clean.ndx
12 -q clean.pdb -[no]h -[no]version -nice int -chainsep enum -ff string
13 -water enum -[no]inter -[no]ss -[no]ter -[no]lys -[no]arg -[no]asp
14 -[no]glu -[no]gln -[no]his -angle real -dist real -[no]una -[no]ignh
15 -[no]missing -[no]v -posrefc real -vsite enum -[no]heavyh -[no]deuter‐
16 ate -[no]chargegrp -[no]cmap -[no]renum -[no]rtpres
17
19 This program reads a pdb (or gro) file, reads some database files, adds
20 hydrogens to the molecules and generates coordinates in Gromacs (Gro‐
21 mos), or optionally pdb, format and a topology in Gromacs format.
22 These files can subsequently be processed to generate a run input file.
23 pdb2gmx will search for force fields by looking for a forcefield.itp
27 file in subdirectories forcefield.ff of the current working directory
28 and of the Gomracs library directory as inferred from the path of the
29 binary or the GMXLIB environment variable. By default the forcefield
30 selection is interactive, but you can use the -ff option to specify
31 one of the short names in the list on the command line instead. In that
32 case pdb2gmx just looks for the corresponding forcefield.ff directory.
33 After choosing a force field, all files will be read only from the cor‐
37 responding force field directory. If you want to modify or add a
38 residue types, you can copy the force field directory from the Gromacs
39 library directory to your current working directory. If you want to add
40 new protein residue types, you will need to modify residuetypes.dat in
41 the libary directory or copy the whole library directory to a local
42 directory and set the environment variable GMXLIB to the name of that
43 directory. Check chapter 5 of the manual for more information about
44 file formats.
45 Note that a pdb file is nothing more than a file format, and it need
48 not necessarily contain a protein structure. Every kind of molecule for
49 which there is support in the database can be converted. If there is
50 no support in the database, you can add it yourself.
51 The program has limited intelligence, it reads a number of database
54 files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),
55 if necessary this can be done manually. The program can prompt the user
56 to select which kind of LYS, ASP, GLU, CYS or HIS residue she wants.
57 For LYS the choice is between neutral (two protons on NZ) or protonated
58 (three protons, default), for ASP and GLU unprotonated (default) or
59 protonated, for HIS the proton can be either on ND1, on NE2 or on both.
60 By default these selections are done automatically. For His, this is
61 based on an optimal hydrogen bonding conformation. Hydrogen bonds are
62 defined based on a simple geometric criterium, specified by the maximum
63 hydrogen-donor-acceptor angle and donor-acceptor distance, which are
64 set by -angle and -dist respectively.
65 The separation of chains is not entirely trivial since the markup in
68 user-generated PDB files frequently varies and sometimes it is desir‐
69 able to merge entries across a TER record, for instance if you want a
70 disulfide bridge or distance restraints between two protein chains or
71 if you have a HEME group bound to a protein. In such cases multiple
72 chains should be contained in a single molecule_type definition. To
73 handle this, pdb2gmx has an option -chainsep so you can choose whether
74 a new chain should start when we find a TER record, when the chain id
75 changes, combinations of either or both of these or fully interac‐
76 tively.
77 pdb2gmx will also check the occupancy field of the pdb file. If any of
80 the occupancies are not one, indicating that the atom is not resolved
81 well in the structure, a warning message is issued. When a pdb file
82 does not originate from an X-Ray structure determination all occupancy
83 fields may be zero. Either way, it is up to the user to verify the cor‐
84 rectness of the input data (read the article!).
85 During processing the atoms will be reordered according to Gromacs con‐
88 ventions. With -n an index file can be generated that contains one
89 group reordered in the same way. This allows you to convert a Gromos
90 trajectory and coordinate file to Gromos. There is one limitation:
91 reordering is done after the hydrogens are stripped from the input and
92 before new hydrogens are added. This means that you should not use
93 -ignh.
94 The .gro and .g96 file formats do not support chain identifiers.
97 Therefore it is useful to enter a pdb file name at the -o option when
98 you want to convert a multichain pdb file.
99 The option -vsite removes hydrogen and fast improper dihedral motions.
102 Angular and out-of-plane motions can be removed by changing hydrogens
103 into virtual sites and fixing angles, which fixes their position rela‐
104 tive to neighboring atoms. Additionally, all atoms in the aromatic
105 rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS) can be
106 converted into virtual sites, elminating the fast improper dihedral
107 fluctuations in these rings. Note that in this case all other hydrogen
108 atoms are also converted to virtual sites. The mass of all atoms that
109 are converted into virtual sites, is added to the heavy atoms.
110 Also slowing down of dihedral motion can be done with -heavyh done by
113 increasing the hydrogen-mass by a factor of 4. This is also done for
114 water hydrogens to slow down the rotational motion of water. The
115 increase in mass of the hydrogens is subtracted from the bonded (heavy)
116 atom so that the total mass of the system remains the same.
117
119 -f eiwit.pdb Input
120 Structure file: gro g96 pdb tpr etc.
121 -o conf.gro Output
123 Structure file: gro g96 pdb etc.
124 -p topol.top Output
126 Topology file
127 -i posre.itp Output
129 Include file for topology
130 -n clean.ndx Output, Opt.
132 Index file
133 -q clean.pdb Output, Opt.
135 Structure file: gro g96 pdb etc.
136
139 -[no]hno
140 Print help info and quit
141 -[no]versionno
143 Print version info and quit
144 -nice int 0
146 Set the nicelevel
147 -chainsep enum id_or_ter
149 Condition in PDB files when a new chain and molecule_type should be
150 started: id_or_ter, id_and_ter, ter, id or interactive
151 -ff string select
153 Force field, interactive by default. Use -h for information.
154 -water enum select
156 Water model to use: select, none, spc, spce, tip3p, tip4p or
157 tip5p
158 -[no]interno
160 Set the next 8 options to interactive
161 -[no]ssno
163 Interactive SS bridge selection
164 -[no]terno
166 Interactive termini selection, iso charged
167 -[no]lysno
169 Interactive Lysine selection, iso charged
170 -[no]argno
172 Interactive Arganine selection, iso charged
173 -[no]aspno
175 Interactive Aspartic Acid selection, iso charged
176 -[no]gluno
178 Interactive Glutamic Acid selection, iso charged
179 -[no]glnno
181 Interactive Glutamine selection, iso neutral
182 -[no]hisno
184 Interactive Histidine selection, iso checking H-bonds
185 -angle real 135
187 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
188 -dist real 0.3
190 Maximum donor-acceptor distance for a H-bond (nm)
191 -[no]unano
193 Select aromatic rings with united CH atoms on Phenylalanine, Trypto‐
194 phane and Tyrosine
195 -[no]ignhno
197 Ignore hydrogen atoms that are in the pdb file
198 -[no]missingno
200 Continue when atoms are missing, dangerous
201 -[no]vno
203 Be slightly more verbose in messages
204 -posrefc real 1000
206 Force constant for position restraints
207 -vsite enum none
209 Convert atoms to virtual sites: none, hydrogens or aromatics
210 -[no]heavyhno
212 Make hydrogen atoms heavy
213 -[no]deuterateno
215 Change the mass of hydrogens to 2 amu
216 -[no]chargegrpyes
218 Use charge groups in the rtp file
219 -[no]cmapyes
221 Use cmap torsions (if enabled in the rtp file)
222 -[no]renumno
224 Renumber the residues consecutively in the output
225 -[no]rtpresno
227 Use rtp entry names as residue names
228
231 gromacs(7)
232 More information about GROMACS is available at <http://www.gro‐
234 macs.org/>.
235 Thu 26 Aug 2010 pdb2gmx(1)