---
name: "cdist_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "3.3.3-2"
release: "Debian 5.0 (Lenny)"
platforms: ["linux"]
url: "https://new.carta.tech/cdist"
---

# cdist\_d(1)

create input for g\_disco

Part of [cdist(1)](/cdist/1.md).

## NAME

cdist - create input for g\_disco

## 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 reads 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** . This is then used to set 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**

## SEE ALSO

**[gromacs(7)](/gromacs/7.md)**

More information about the **GROMACS** suite is available in **/usr/share/doc/gromacs** or at \<*http://www.gromacs.org/*\>.