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 (but this feature is deprecated). Note
117 that in this case all other hydrogen atoms are also converted to vir‐
118 tual sites. The mass of all atoms that are converted into virtual
119 sites, is added to the heavy atoms.
120 Also slowing down of dihedral motion can be done with -heavyh done by
122 increasing the hydrogen-mass by a factor of 4. This is also done for
123 water hydrogens to slow down the rotational motion of water. The
124 increase in mass of the hydrogens is subtracted from the bonded (heavy)
125 atom so that the total mass of the system remains the same.
126
128 Options to specify input files:
129 -f [<.gro/.g96/…>] (protein.pdb)
131 Structure file: gro g96 pdb brk ent esp tpr
132 Options to specify output files:
134 -o [<.gro/.g96/…>] (conf.gro)
136 Structure file: gro g96 pdb brk ent esp
137 -p [<.top>] (topol.top)
139 Topology file
140 -i [<.itp>] (posre.itp)
142 Include file for topology
143 -n [<.ndx>] (index.ndx) (Optional)
145 Index file
146 -q [<.gro/.g96/…>] (clean.pdb) (Optional)
148 Structure file: gro g96 pdb brk ent esp
149 Other options:
151 -chainsep <enum> (id_or_ter)
153 Condition in PDB files when a new chain should be started
154 (adding termini): id_or_ter, id_and_ter, ter, id, interactive
155 -merge <enum> (no)
157 Merge multiple chains into a single [moleculetype]: no, all,
158 interactive
159 -ff <string> (select)
161 Force field, interactive by default. Use -h for information.
162 -water <enum> (select)
164 Water model to use: select, none, spc, spce, tip3p, tip4p,
165 tip5p, tips3p
166 -[no]inter (no)
168 Set the next 8 options to interactive
169 -[no]ss (no)
171 Interactive SS bridge selection
172 -[no]ter (no)
174 Interactive termini selection, instead of charged (default)
175 -[no]lys (no)
177 Interactive lysine selection, instead of charged
178 -[no]arg (no)
180 Interactive arginine selection, instead of charged
181 -[no]asp (no)
183 Interactive aspartic acid selection, instead of charged
184 -[no]glu (no)
186 Interactive glutamic acid selection, instead of charged
187 -[no]gln (no)
189 Interactive glutamine selection, instead of charged
190 -[no]his (no)
192 Interactive histidine selection, instead of checking H-bonds
193 -angle <real> (135)
195 Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
196 -dist <real> (0.3)
198 Maximum donor-acceptor distance for a H-bond (nm)
199 -[no]una (no)
201 Select aromatic rings with united CH atoms on phenylalanine,
202 tryptophane and tyrosine
203 -[no]ignh (no)
205 Ignore hydrogen atoms that are in the coordinate file
206 -[no]missing (no)
208 Continue when atoms are missing and bonds cannot be made, dan‐
209 gerous
210 -[no]v (no)
212 Be slightly more verbose in messages
213 -posrefc <real> (1000)
215 Force constant for position restraints
216 -vsite <enum> (none)
218 Convert atoms to virtual sites: none, hydrogens, aromatics
219 -[no]heavyh (no)
221 Make hydrogen atoms heavy
222 -[no]deuterate (no)
224 Change the mass of hydrogens to 2 amu
225 -[no]chargegrp (yes)
227 Use charge groups in the .rtp file
228 -[no]cmap (yes)
230 Use cmap torsions (if enabled in the .rtp file)
231 -[no]renum (no)
233 Renumber the residues consecutively in the output
234 -[no]rtpres (no)
236 Use .rtp entry names as residue names
237
239 gmx(1)
240 More information about GROMACS is available at <‐
242 http://www.gromacs.org/>.
243
245 2019, GROMACS development team
2462019.2 Apr 16, 2019 GMX-PDB2GMX(1)