1 .TH pdb2gmx 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-3c0e5ec"
3 pdb2gmx - converts pdb files to topology and coordinate files
5 .B VERSION 4.5.4-dev-20110404-3c0e5ec
8 .BI "\-f" " eiwit.pdb "
10 .BI "\-p" " topol.top "
11 .BI "\-i" " posre.itp "
12 .BI "\-n" " clean.ndx "
13 .BI "\-q" " clean.pdb "
15 .BI "\-[no]version" ""
17 .BI "\-chainsep" " enum "
19 .BI "\-water" " enum "
29 .BI "\-angle" " real "
33 .BI "\-[no]missing" ""
35 .BI "\-posrefc" " real "
36 .BI "\-vsite" " enum "
38 .BI "\-[no]deuterate" ""
39 .BI "\-[no]chargegrp" ""
44 \&This program reads a \fB .pdb\fR (or \fB .gro\fR) file, reads
45 \&some database files, adds hydrogens to the molecules and generates
46 \&coordinates in GROMACS (GROMOS), or optionally \fB .pdb\fR, format
47 \&and a topology in GROMACS format.
48 \&These files can subsequently be processed to generate a run input file.
52 \&\fB pdb2gmx\fR will search for force fields by looking for
53 \&a \fB forcefield.itp\fR file in subdirectories \fB forcefield.ff\fR
54 \&of the current working directory and of the Gromacs library directory
55 \&as inferred from the path of the binary or the \fB GMXLIB\fR environment
57 \&By default the forcefield selection is interactive,
58 \&but you can use the \fB \-ff\fR option to specify one of the short names
59 \&in the list on the command line instead. In that case \fB pdb2gmx\fR just looks
60 \&for the corresponding \fB forcefield.ff\fR directory.
64 \&After choosing a force field, all files will be read only from
65 \&the corresponding force field directory.
66 \&If you want to modify or add a residue types, you can copy the force
67 \&field directory from the Gromacs library directory to your current
68 \&working directory. If you want to add new protein residue types,
69 \&you will need to modify \fB residuetypes.dat\fR in the library directory
70 \&or copy the whole library directory to a local directory and set
71 \&the environment variable \fB GMXLIB\fR to the name of that directory.
72 \&Check Chapter 5 of the manual for more information about file formats.
76 \&Note that a \fB .pdb\fR file is nothing more than a file format, and it
77 \&need not necessarily contain a protein structure. Every kind of
78 \&molecule for which there is support in the database can be converted.
79 \&If there is no support in the database, you can add it yourself.
82 \&The program has limited intelligence, it reads a number of database
83 \&files, that allow it to make special bonds (Cys\-Cys, Heme\-His, etc.),
84 \&if necessary this can be done manually. The program can prompt the
85 \&user to select which kind of LYS, ASP, GLU, CYS or HIS residue she
86 \&wants. For LYS the choice is between neutral (two protons on NZ) or
87 \&protonated (three protons, default), for ASP and GLU unprotonated
88 \&(default) or protonated, for HIS the proton can be either on ND1,
89 \&on NE2 or on both. By default these selections are done automatically.
90 \&For His, this is based on an optimal hydrogen bonding
91 \&conformation. Hydrogen bonds are defined based on a simple geometric
92 \&criterion, specified by the maximum hydrogen\-donor\-acceptor angle
93 \&and donor\-acceptor distance, which are set by \fB \-angle\fR and
94 \&\fB \-dist\fR respectively.
97 \&The separation of chains is not entirely trivial since the markup
98 \&in user\-generated PDB files frequently varies and sometimes it
99 \&is desirable to merge entries across a TER record, for instance
100 \&if you want a disulfide bridge or distance restraints between
101 \&two protein chains or if you have a HEME group bound to a protein.
102 \&In such cases multiple chains should be contained in a single
103 \&\fB moleculetype\fR definition.
104 \&To handle this, \fB pdb2gmx\fR has an option \fB \-chainsep\fR so you can
105 \&choose whether a new chain should start when we find a TER record,
106 \&when the chain id changes, combinations of either or both of these
107 \&or fully interactively.
110 \&\fB pdb2gmx\fR will also check the occupancy field of the \fB .pdb\fR file.
111 \&If any of the occupancies are not one, indicating that the atom is
112 \¬ resolved well in the structure, a warning message is issued.
113 \&When a \fB .pdb\fR file does not originate from an X\-ray structure determination
114 \&all occupancy fields may be zero. Either way, it is up to the user
115 \&to verify the correctness of the input data (read the article!).
118 \&During processing the atoms will be reordered according to GROMACS
119 \&conventions. With \fB \-n\fR an index file can be generated that
120 \&contains one group reordered in the same way. This allows you to
121 \&convert a GROMOS trajectory and coordinate file to GROMOS. There is
122 \&one limitation: reordering is done after the hydrogens are stripped
123 \&from the input and before new hydrogens are added. This means that
124 \&you should not use \fB \-ignh\fR.
127 \&The \fB .gro\fR and \fB .g96\fR file formats do not support chain
128 \&identifiers. Therefore it is useful to enter a \fB .pdb\fR file name at
129 \&the \fB \-o\fR option when you want to convert a multi\-chain \fB .pdb\fR file.
133 \&The option \fB \-vsite\fR removes hydrogen and fast improper dihedral
134 \&motions. Angular and out\-of\-plane motions can be removed by changing
135 \&hydrogens into virtual sites and fixing angles, which fixes their
136 \&position relative to neighboring atoms. Additionally, all atoms in the
137 \&aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS)
138 \&can be converted into virtual sites, eliminating the fast improper dihedral
139 \&fluctuations in these rings. \fB Note\fR that in this case all other hydrogen
140 \&atoms are also converted to virtual sites. The mass of all atoms that are
141 \&converted into virtual sites, is added to the heavy atoms.
144 \&Also slowing down of dihedral motion can be done with \fB \-heavyh\fR
145 \&done by increasing the hydrogen\-mass by a factor of 4. This is also
146 \&done for water hydrogens to slow down the rotational motion of water.
147 \&The increase in mass of the hydrogens is subtracted from the bonded
148 \&(heavy) atom so that the total mass of the system remains the same.
150 .BI "\-f" " eiwit.pdb"
152 Structure file: gro g96 pdb tpr etc.
154 .BI "\-o" " conf.gro"
156 Structure file: gro g96 pdb etc.
158 .BI "\-p" " topol.top"
162 .BI "\-i" " posre.itp"
164 Include file for topology
166 .BI "\-n" " clean.ndx"
170 .BI "\-q" " clean.pdb"
172 Structure file: gro g96 pdb etc.
176 Print help info and quit
178 .BI "\-[no]version" "no "
179 Print version info and quit
181 .BI "\-nice" " int" " 0"
184 .BI "\-chainsep" " enum" " id_or_ter"
185 Condition in PDB files when a new chain and molecule_type should be started: \fB id_or_ter\fR, \fB id_and_ter\fR, \fB ter\fR, \fB id\fR or \fB interactive\fR
187 .BI "\-ff" " string" " select"
188 Force field, interactive by default. Use \fB \-h\fR for information.
190 .BI "\-water" " enum" " select"
191 Water model to use: \fB select\fR, \fB none\fR, \fB spc\fR, \fB spce\fR, \fB tip3p\fR, \fB tip4p\fR or \fB tip5p\fR
193 .BI "\-[no]inter" "no "
194 Set the next 8 options to interactive
197 Interactive SS bridge selection
199 .BI "\-[no]ter" "no "
200 Interactive termini selection, iso charged
202 .BI "\-[no]lys" "no "
203 Interactive lysine selection, iso charged
205 .BI "\-[no]arg" "no "
206 Interactive arginine selection, iso charged
208 .BI "\-[no]asp" "no "
209 Interactive aspartic Acid selection, iso charged
211 .BI "\-[no]glu" "no "
212 Interactive glutamic Acid selection, iso charged
214 .BI "\-[no]gln" "no "
215 Interactive glutamine selection, iso neutral
217 .BI "\-[no]his" "no "
218 Interactive histidine selection, iso checking H\-bonds
220 .BI "\-angle" " real" " 135 "
221 Minimum hydrogen\-donor\-acceptor angle for a H\-bond (degrees)
223 .BI "\-dist" " real" " 0.3 "
224 Maximum donor\-acceptor distance for a H\-bond (nm)
226 .BI "\-[no]una" "no "
227 Select aromatic rings with united CH atoms on phenylalanine, tryptophane and tyrosine
229 .BI "\-[no]ignh" "no "
230 Ignore hydrogen atoms that are in the coordinate file
232 .BI "\-[no]missing" "no "
233 Continue when atoms are missing, dangerous
236 Be slightly more verbose in messages
238 .BI "\-posrefc" " real" " 1000 "
239 Force constant for position restraints
241 .BI "\-vsite" " enum" " none"
242 Convert atoms to virtual sites: \fB none\fR, \fB hydrogens\fR or \fB aromatics\fR
244 .BI "\-[no]heavyh" "no "
245 Make hydrogen atoms heavy
247 .BI "\-[no]deuterate" "no "
248 Change the mass of hydrogens to 2 amu
250 .BI "\-[no]chargegrp" "yes "
251 Use charge groups in the \fB .rtp\fR file
253 .BI "\-[no]cmap" "yes "
254 Use cmap torsions (if enabled in the \fB .rtp\fR file)
256 .BI "\-[no]renum" "no "
257 Renumber the residues consecutively in the output
259 .BI "\-[no]rtpres" "no "
260 Use \fB .rtp\fR entry names as residue names
265 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.