man cdist (Commandes) - cdist VERSION 3.3_beta_20050823
NAME
cdist VERSION 3.3_beta_20050823
SYNOPSIS
cdist -s topol.tpr -g cdist.log -q eiwit.pdb -d nnnice.dat -o cdist.dat -n hbond.ndx -dom domain.ndx -[no]h -nice int -[no]engh -bm real -am real -pm real -rr real -ar real -er real -vm real -lm real -il real -dm real -im real -nm real -hm real -hb real -[no]bon -[no]nb -measure real -maxdist real -[no]add -[no]vir -sm enum
DESCRIPTION
cdist read a tpx file and dumps an input file for disco. Bond lengths etc. are read from the topology. Pairs of atoms that can form hydrogen bonds are given a lowest possible distance of
hblen (can be specified by the user). Other nonbonded pairs take their minimum distance from the Lennard Jones parameters (at the combined sigma).
The program uses proper dihedrals to give a distance too, as minimum respectively maximum the cis and trans configurations are taken. It is therefore beneficial to use the -alldih option of pdb2gmx to generate a topology with all dihedrals in there. If the optional pdb file is given, weights are read from the occupancy field, so that not all atoms are part of the disco run, only those of which one of the weights is non-zero.
If the option -engh is on (default) bond lengths and angles etc. are read from another database, which is basically the Engh-Huber data but refined to be completely self consistent. The database name is refi_aa.dat and it resides in the $GMXLIB directory, or in the current directory.
The program can read a file with distances from NMR distance restraints (-d option). Note that these distance are treated slightly different in the disco program, and therefore these distance should be NMR derived distance restraints only.
Furthermore, the program can read an index file with hydrogen bond information as generated by g_hbond tighter restraints on the hydrogen bonded atoms than on the other non bonded atom pairs, in order to maintain secondary structure. This option is useful only in combination with the -measure
option, when a sensible structure is known.
The option -dom can be used to release distances bounds between different domains to the lower bounds given by Van der Waals contacts. This way, different domains can move independently, but without overlapping. The index file should contain domains that do not overlap with each other.
FILES
-s topol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-g cdist.log Output Log file
-q eiwit.pdb Input, Opt. Protein data bank file
-d nnnice.dat Input, Opt. Generic data file
-o cdist.dat Output Generic data file
-n hbond.ndx Input, Opt. Index file
-dom domain.ndx Input, Opt. Index file
OTHER OPTIONS
-[no]h no Print help info and quit
-nice int 0 Set the nicelevel
-[no]engh yes Use the Engh&Huber parameters for bond-lengths etc.
-bm real 0.01 Relative margin for bond lengths
-am real 0.01 Relative margin for bond angle lengths
-pm real 0.01 Relative margin for peptidebond dihedrals
-rr real 0.01 Relative margin to keep rings flat (trp,tyr,phe,hisb)
-ar real 0.01 Relative margin for arginine
-er real 0.01 Relative margin for asn and gln
-vm real 0.01 Relative margin for valine (0 disables)
-lm real 0.01 Relative margin for leucine (0 disables)
-il real 0.03 Relative margin for isoleucine (0 disables)
-dm real 0.01 !inactive! Relative margin for dihedral lengths
-im real 0.01 Relative margin for improper dihedral lengths
-nm real 0.05 Relative margin for nonbonded lower bounds
-hm real 0.02 Relative margin for hydrogen bonded atoms, which must be specified in an index file, as generated by g_hbond
-hb real 2.3 Shortest possible distance for a hydrogen bond (in Angstrom!)
-[no]bon yes Make bonded distance constraints
-[no]nb yes Make nonbonded distance constraints (lower bound only)
-measure real 0 Add (nonbonded) distances by examining all atoms within the distance given (in Angstrom), and using the margin given by the -nm option.
-maxdist real 0 Maximum distance between any pair of atoms
-[no]add no Write restraints in format of additional restraints for disco
-[no]vir no Use virtual particles
-sm enum none Smoothing: none, tri (Using triangle inequality), or tetra (Partial tetrangle inequaliy): none , tri or tetra