1GMX-PDB2GMX(1) GROMACS GMX-PDB2GMX(1)
2
6 gmx-pdb2gmx - Convert coordinate files to topology and FF-compliant co‐
7 ordinate 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-), re‐
65 spectively. Some force fields support zwitterionic forms for chains of
66 one residue, but for polypeptides these options should NOT be selected.
67 The AMBER force fields have unique forms for the terminal residues, and
68 these are incompatible with the -ter mechanism. You need to prefix your
69 N- or C-terminal residue names with "N" or "C" respectively to use
70 these forms, making sure you preserve the format of the coordinate
71 file. Alternatively, use named terminating residues (e.g. ACE, NME).
72 The separation of chains is not entirely trivial since the markup in
74 user-generated PDB files frequently varies and sometimes it is desir‐
75 able to merge entries across a TER record, for instance if you want a
76 disulfide bridge or distance restraints between two protein chains or
77 if you have a HEME group bound to a protein. In such cases multiple
78 chains should be contained in a single moleculetype definition. To
79 handle this, gmx pdb2gmx uses two separate options. First, -chainsep
80 allows you to choose when a new chemical chain should start, and ter‐
81 mini added when applicable. This can be done based on the existence of
82 TER records, when the chain id changes, or combinations of either or
83 both of these. You can also do the selection fully interactively. In
84 addition, there is a -merge option that controls how multiple chains
85 are merged into one moleculetype, after adding all the chemical termini
86 (or not). This can be turned off (no merging), all non-water chains
87 can be merged into a single molecule, or the selection can be done in‐
88 teractively.
89 gmx pdb2gmx will also check the occupancy field of the .pdb file. If
91 any of the occupancies are not one, indicating that the atom is not re‐
92 solved well in the structure, a warning message is issued. When a .pdb
93 file does not originate from an X-ray structure determination all occu‐
94 pancy fields may be zero. Either way, it is up to the user to verify
95 the correctness of the input data (read the article!).
96 During processing the atoms will be reordered according to GROMACS con‐
98 ventions. With -n an index file can be generated that contains one
99 group reordered in the same way. This allows you to convert a GROMOS
100 trajectory and coordinate file to GROMOS. There is one limitation: re‐
101 ordering is done after the hydrogens are stripped from the input and
102 before new hydrogens are added. This means that you should not use
103 -ignh.
104 The .gro and .g96 file formats do not support chain identifiers. There‐
106 fore it is useful to enter a .pdb file name at the -o option when you
107 want to convert a multi-chain .pdb file.
108 The option -vsite removes hydrogen and fast improper dihedral motions.
110 Angular and out-of-plane motions can be removed by changing hydrogens
111 into virtual sites and fixing angles, which fixes their position rela‐
112 tive to neighboring atoms. Additionally, all atoms in the aromatic
113 rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS) can be
114 converted into virtual sites, eliminating the fast improper dihedral
115 fluctuations in these rings (but this feature is deprecated). Note
116 that in this case all other hydrogen atoms are also converted to vir‐
117 tual sites. The mass of all atoms that are converted into virtual
118 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 in‐
123 crease in mass of the hydrogens is subtracted from the bonded (heavy)
124 atom so that the total mass of the system remains the same. As a spe‐
125 cial case, ring-closed (or cyclic) molecules are considered. gmx
126 pdb2gmx automatically determines if a cyclic molecule is present by
127 evaluating the distance between the terminal atoms of a given chain.
128 If this distance is greater than the -sb ("Short bond warning dis‐
129 tance", default 0.05 nm) and less than the -lb ("Long bond warning dis‐
130 tance", default 0.25 nm) the molecule is considered to be ring closed
131 and will be processed as such. Please note that this does not detect
132 cyclic bonds over periodic boundaries.
133
135 Options to specify input files:
136 -f [<.gro/.g96/...>] (protein.pdb)
138 Structure file: gro g96 pdb brk ent esp tpr
139 Options to specify output files:
141 -o [<.gro/.g96/...>] (conf.gro)
143 Structure file: gro g96 pdb brk ent esp
144 -p [<.top>] (topol.top)
146 Topology file
147 -i [<.itp>] (posre.itp)
149 Include file for topology
150 -n [<.ndx>] (index.ndx) (Optional)
152 Index file
153 -q [<.gro/.g96/...>] (clean.pdb) (Optional)
155 Structure file: gro g96 pdb brk ent esp
156 Other options:
158 -chainsep <enum> (id_or_ter)
160 Condition in PDB files when a new chain should be started
161 (adding termini): id_or_ter, id_and_ter, ter, id, interactive
162 -merge <enum> (no)
164 Merge multiple chains into a single [moleculetype]: no, all, in‐
165 teractive
166 -ff <string> (select)
168 Force field, interactive by default. Use -h for information.
169 -water <enum> (select)
171 Water model to use: select, none, spc, spce, tip3p, tip4p,
172 tip5p, tips3p
173 -[no]inter (no)
175 Set the next 8 options to interactive
176 -[no]ss (no)
178 Interactive SS bridge selection
179 -[no]ter (no)
181 Interactive termini selection, instead of charged (default)
182 -[no]lys (no)
184 Interactive lysine selection, instead of charged
185 -[no]arg (no)
187 Interactive arginine selection, instead of charged
188 -[no]asp (no)
190 Interactive aspartic acid selection, instead of charged
191 -[no]glu (no)
193 Interactive glutamic acid selection, instead of charged
194 -[no]gln (no)
196 Interactive glutamine selection, instead of charged
197 -[no]his (no)
199 Interactive histidine selection, instead of checking H-bonds
200 -angle <real> (135)
202 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
203 -dist <real> (0.3)
205 Maximum donor-acceptor distance for a H-bond (nm)
206 -[no]una (no)
208 Select aromatic rings with united CH atoms on phenylalanine,
209 tryptophane and tyrosine
210 -[no]ignh (no)
212 Ignore hydrogen atoms that are in the coordinate file
213 -[no]missing (no)
215 Continue when atoms are missing and bonds cannot be made, dan‐
216 gerous
217 -[no]v (no)
219 Be slightly more verbose in messages
220 -posrefc <real> (1000)
222 Force constant for position restraints
223 -vsite <enum> (none)
225 Convert atoms to virtual sites: none, hydrogens, aromatics
226 -[no]heavyh (no)
228 Make hydrogen atoms heavy
229 -[no]deuterate (no)
231 Change the mass of hydrogens to 2 amu
232 -[no]chargegrp (yes)
234 Use charge groups in the .rtp file
235 -[no]cmap (yes)
237 Use cmap torsions (if enabled in the .rtp file)
238 -[no]renum (no)
240 Renumber the residues consecutively in the output
241 -[no]rtpres (no)
243 Use .rtp entry names as residue names
244
246 gmx(1)
247 More information about GROMACS is available at <‐
249 http://www.gromacs.org/>.
250
252 2022, GROMACS development team
2532022.3 Sep 02, 2022 GMX-PDB2GMX(1)