1GMX-PDB2GMX(1) GROMACS GMX-PDB2GMX(1)
2
6 gmx-pdb2gmx - Convert coordinate files to topology and FF-compliant
7 coordinate files
8
10 gmx pdb2gmx [-f [<.gro/.g96/...>]] [-o [<.gro/.g96/...>]] [-p [<.top>]]
11 [-i [<.itp>]] [-n [<.ndx>]] [-q [<.gro/.g96/...>]]
12 [-chainsep <enum>] [-merge <enum>] [-ff <string>]
13 [-water <enum>] [-[no]inter] [-[no]ss] [-[no]ter]
14 [-[no]lys] [-[no]arg] [-[no]asp] [-[no]glu] [-[no]gln]
15 [-[no]his] [-angle <real>] [-dist <real>] [-[no]una]
16 [-[no]ignh] [-[no]missing] [-[no]v] [-posrefc <real>]
17 [-vsite <enum>] [-[no]heavyh] [-[no]deuterate]
18 [-[no]chargegrp] [-[no]cmap] [-[no]renum] [-[no]rtpres]
19
21 gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,
22 adds hydrogens to the molecules and generates coordinates in GROMACS
23 (GROMOS), or optionally .pdb, format and a topology in GROMACS format.
24 These files can subsequently be processed to generate a run input file.
25 gmx pdb2gmx will search for force fields by looking for a force‐
27 field.itp file in subdirectories <forcefield>.ff of the current working
28 directory and of the GROMACS library directory as inferred from the
29 path of the binary or the GMXLIB environment variable. By default the
30 forcefield selection is interactive, but you can use the -ff option to
31 specify one of the short names in the list on the command line instead.
32 In that case gmx pdb2gmx just looks for the corresponding <force‐
33 field>.ff directory.
34 After choosing a force field, all files will be read only from the cor‐
36 responding force field directory. If you want to modify or add a
37 residue types, you can copy the force field directory from the GROMACS
38 library directory to your current working directory. If you want to add
39 new protein residue types, you will need to modify residuetypes.dat in
40 the library directory or copy the whole library directory to a local
41 directory and set the environment variable GMXLIB to the name of that
42 directory. Check Chapter 5 of the manual for more information about
43 file formats.
44 Note that a .pdb file is nothing more than a file format, and it need
46 not necessarily contain a protein structure. Every kind of molecule for
47 which there is support in the database can be converted. If there is
48 no support in the database, you can add it yourself.
49 The program has limited intelligence, it reads a number of database
51 files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.),
52 if necessary this can be done manually. The program can prompt the user
53 to select which kind of LYS, ASP, GLU, CYS or HIS residue is desired.
54 For Lys the choice is between neutral (two protons on NZ) or protonated
55 (three protons, default), for Asp and Glu unprotonated (default) or
56 protonated, for His the proton can be either on ND1, on NE2 or on both.
57 By default these selections are done automatically. For His, this is
58 based on an optimal hydrogen bonding conformation. Hydrogen bonds are
59 defined based on a simple geometric criterion, specified by the maximum
60 hydrogen-donor-acceptor angle and donor-acceptor distance, which are
61 set by -angle and -dist respectively.
62 The protonation state of N- and C-termini can be chosen interactively
64 with the -ter flag. Default termini are ionized (NH3+ and COO-),
65 respectively. Some force fields support zwitterionic forms for chains
66 of one residue, but for polypeptides these options should NOT be
67 selected. The AMBER force fields have unique forms for the terminal
68 residues, and these are incompatible with the -ter mechanism. You need
69 to prefix your N- or C-terminal residue names with “N” or “C” respec‐
70 tively to use these forms, making sure you preserve the format of the
71 coordinate file. Alternatively, use named terminating residues (e.g.
72 ACE, NME).
73 The separation of chains is not entirely trivial since the markup in
75 user-generated PDB files frequently varies and sometimes it is desir‐
76 able to merge entries across a TER record, for instance if you want a
77 disulfide bridge or distance restraints between two protein chains or
78 if you have a HEME group bound to a protein. In such cases multiple
79 chains should be contained in a single moleculetype definition. To
80 handle this, gmx pdb2gmx uses two separate options. First, -chainsep
81 allows you to choose when a new chemical chain should start, and ter‐
82 mini added when applicable. This can be done based on the existence of
83 TER records, when the chain id changes, or combinations of either or
84 both of these. You can also do the selection fully interactively. In
85 addition, there is a -merge option that controls how multiple chains
86 are merged into one moleculetype, after adding all the chemical termini
87 (or not). This can be turned off (no merging), all non-water chains
88 can be merged into a single molecule, or the selection can be done
89 interactively.
90 gmx pdb2gmx will also check the occupancy field of the .pdb file. If
92 any of the occupancies are not one, indicating that the atom is not
93 resolved well in the structure, a warning message is issued. When a
94 .pdb file does not originate from an X-ray structure determination all
95 occupancy fields may be zero. Either way, it is up to the user to ver‐
96 ify the correctness of the input data (read the article!).
97 During processing the atoms will be reordered according to GROMACS con‐
99 ventions. With -n an index file can be generated that contains one
100 group reordered in the same way. This allows you to convert a GROMOS
101 trajectory and coordinate file to GROMOS. There is one limitation:
102 reordering is done after the hydrogens are stripped from the input and
103 before new hydrogens are added. This means that you should not use
104 -ignh.
105 The .gro and .g96 file formats do not support chain identifiers. There‐
107 fore it is useful to enter a .pdb file name at the -o option when you
108 want to convert a multi-chain .pdb file.
109 The option -vsite removes hydrogen and fast improper dihedral motions.
111 Angular and out-of-plane motions can be removed by changing hydrogens
112 into virtual sites and fixing angles, which fixes their position rela‐
113 tive to neighboring atoms. Additionally, all atoms in the aromatic
114 rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS) can be
115 converted into virtual sites, eliminating the fast improper dihedral
116 fluctuations in these rings. Note that in this case all other hydrogen
117 atoms are also converted to virtual sites. The mass of all atoms that
118 are converted into virtual sites, is added to the heavy atoms.
119 Also slowing down of dihedral motion can be done with -heavyh done by
121 increasing the hydrogen-mass by a factor of 4. This is also done for
122 water hydrogens to slow down the rotational motion of water. The
123 increase in mass of the hydrogens is subtracted from the bonded (heavy)
124 atom so that the total mass of the system remains the same.
125
127 Options to specify input files:
128 -f [<.gro/.g96/…>] (eiwit.pdb)
130 Structure file: gro g96 pdb brk ent esp tpr
131 Options to specify output files:
133 -o [<.gro/.g96/…>] (conf.gro)
135 Structure file: gro g96 pdb brk ent esp
136 -p [<.top>] (topol.top)
138 Topology file
139 -i [<.itp>] (posre.itp)
141 Include file for topology
142 -n [<.ndx>] (clean.ndx) (Optional)
144 Index file
145 -q [<.gro/.g96/…>] (clean.pdb) (Optional)
147 Structure file: gro g96 pdb brk ent esp
148 Other options:
150 -chainsep <enum> (id_or_ter)
152 Condition in PDB files when a new chain should be started
153 (adding termini): id_or_ter, id_and_ter, ter, id, interactive
154 -merge <enum> (no)
156 Merge multiple chains into a single [moleculetype]: no, all,
157 interactive
158 -ff <string> (select)
160 Force field, interactive by default. Use -h for information.
161 -water <enum> (select)
163 Water model to use: select, none, spc, spce, tip3p, tip4p,
164 tip5p, tips3p
165 -[no]inter (no)
167 Set the next 8 options to interactive
168 -[no]ss (no)
170 Interactive SS bridge selection
171 -[no]ter (no)
173 Interactive termini selection, instead of charged (default)
174 -[no]lys (no)
176 Interactive lysine selection, instead of charged
177 -[no]arg (no)
179 Interactive arginine selection, instead of charged
180 -[no]asp (no)
182 Interactive aspartic acid selection, instead of charged
183 -[no]glu (no)
185 Interactive glutamic acid selection, instead of charged
186 -[no]gln (no)
188 Interactive glutamine selection, instead of neutral
189 -[no]his (no)
191 Interactive histidine selection, instead of checking H-bonds
192 -angle <real> (135)
194 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
195 -dist <real> (0.3)
197 Maximum donor-acceptor distance for a H-bond (nm)
198 -[no]una (no)
200 Select aromatic rings with united CH atoms on phenylalanine,
201 tryptophane and tyrosine
202 -[no]ignh (no)
204 Ignore hydrogen atoms that are in the coordinate file
205 -[no]missing (no)
207 Continue when atoms are missing and bonds cannot be made, dan‐
208 gerous
209 -[no]v (no)
211 Be slightly more verbose in messages
212 -posrefc <real> (1000)
214 Force constant for position restraints
215 -vsite <enum> (none)
217 Convert atoms to virtual sites: none, hydrogens, aromatics
218 -[no]heavyh (no)
220 Make hydrogen atoms heavy
221 -[no]deuterate (no)
223 Change the mass of hydrogens to 2 amu
224 -[no]chargegrp (yes)
226 Use charge groups in the .rtp file
227 -[no]cmap (yes)
229 Use cmap torsions (if enabled in the .rtp file)
230 -[no]renum (no)
232 Renumber the residues consecutively in the output
233 -[no]rtpres (no)
235 Use .rtp entry names as residue names
236
238 gmx(1)
239 More information about GROMACS is available at <‐
241 http://www.gromacs.org/>.
242
244 2019, GROMACS development team
2452018.7 May 29, 2019 GMX-PDB2GMX(1)