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3.3. Nchemgrids
Nchemgrids


    AUTHOR: Xiaoqin Zou
AUTHOR: Xiaoqin Zou


    USAGE: nchemgrid_GB or nchemgrid_SA
USAGE: nchemgrid_GB or nchemgrid_SA


    INPUT FILE:
= INPUT FILE =


    Both programs require that an INCHEM file be created in the working directory, which contains the parameters to control the program. The INCHEM parameters for both the nchemgrid_GB and nchemgrid_SA programs are detailed below:
Both programs require that an INCHEM file be created in the working directory, which contains the parameters to control the program. The INCHEM parameters for both the nchemgrid_GB and nchemgrid_SA programs are detailed below:


    For nchemgrid_GB:
For nchemgrid_GB:


         receptor.pdb ; receptor pdb file
         receptor.pdb ; receptor pdb file
Line 25: Line 25:
         1 ; pairwise calculation
         1 ; pairwise calculation


    NOTE: The cavity.pdb file should be an empty file. This feature is not frequently used. However, the parameter must still be passed. The pairwise calculation value must also always be 1.
NOTE: The cavity.pdb file should be an empty file. This feature is not frequently used. However, the parameter must still be passed. The pairwise calculation value must also always be 1.


    For nchemgrid_SA:
For nchemgrid_SA:


         receptor.pdb ; receptor pdb file
         receptor.pdb ; receptor pdb file
Line 39: Line 39:
         output_prefix ; output grid prefix name
         output_prefix ; output grid prefix name


    DESCRIPTION:
= DESCRIPTION =


    The nchemgrid_gb and nchemgrid_sa programs create the GB and SA receptor grids for use with the Zou GB/SA scoring function (see Zou GB/SA Scoring).
The nchemgrid_gb and nchemgrid_sa programs create the GB and SA receptor grids for use with the Zou GB/SA scoring function (see Zou GB/SA Scoring).


    OUTPUT FILES
= OUTPUT FILES =


     For nchemgrid_gb
     For nchemgrid_gb
* inva #debugging file with inverse Born radius for receptor atoms
* NEG_INVA #error file listing embedded receptor atoms
* OUTCHEM #restatement of input parameters; messages pertaining to calculation of the grids
* OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
* PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file
screen.para #file that contains descreening parameters
* zou_grid.bmp #bump grid
* zou_grid.rec #xyz coordinates, effective charge, effective vdw radii, inverse Born radii, and descreening parameters for receptor
* zou_grid.sol #flags for whether receptor atoms are solvated
* zou_grid.vdw #vdw values for receptor


        * inva #debugging file with inverse Born radius for receptor atoms
For nchemgrid_sa:
        * NEG_INVA #error file listing embedded receptor atoms
* OUTCHEM #restatement of input parameters; messages pertaining to calculation of the grids
        * OUTCHEM #restatement of input parameters; messages pertaining to calculation of the grids
* OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
        * OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
* PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file
        * PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file
* zou_grid.bmp #bump grid
          screen.para #file that contains descreening parameters
* zou_grid.sas #xyz coordinates, effective vdw radii, vdw type, number of spherical grid points, and polarity type for each receptor atom
        * zou_grid.bmp #bump grid
* zou_grid.sasmark #information about grid spacing, coordinates, dimensions, etc
        * zou_grid.rec #xyz coordinates, effective charge, effective vdw radii, inverse Born radii, and descreening parameters for receptor
        * zou_grid.sol #flags for whether receptor atoms are solvated
        * zou_grid.vdw #vdw values for receptor


    For nchemgrid_sa:
[[Category:DOCK 6]]
 
        * OUTCHEM #restatement of input parameters; messages pertaining to calculation of the grids
        * OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
        * PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file
        * zou_grid.bmp #bump grid
        * zou_grid.sas #xyz coordinates, effective vdw radii, vdw type, number of spherical grid points, and polarity type for each receptor atom
        * zou_grid.sasmark #information about grid spacing, coordinates, dimensions, etc

Latest revision as of 17:44, 15 February 2014

Nchemgrids

AUTHOR: Xiaoqin Zou

USAGE: nchemgrid_GB or nchemgrid_SA

INPUT FILE

Both programs require that an INCHEM file be created in the working directory, which contains the parameters to control the program. The INCHEM parameters for both the nchemgrid_GB and nchemgrid_SA programs are detailed below:

For nchemgrid_GB: 

       receptor.pdb ; receptor pdb file
       cavity.pdb ; cavity pdb file
       parameters/ prot.table.ambcrg.ambH ; charge parameter file
       parameters/ vdw.parms.amb ; VDW parameter file
       box.pdb ; box pdb file
       0.4 ; grid spacing in angstroms
       2 ; es type: GB
       1 ; es scale for ff scoring
       8.0 8.0 ; cutoff for es and outer box
       78.3 78.3 ; dielectric of solvent ,cavity
       2.3 2.8 ; bumping distances
       output_prefix ; output grid prefix name
       1 ; pairwise calculation

NOTE: The cavity.pdb file should be an empty file. This feature is not frequently used. However, the parameter must still be passed. The pairwise calculation value must also always be 1.

For nchemgrid_SA: 

       receptor.pdb ; receptor pdb file
       parameters/prot.table.ambcrg.ambH ; charge parameter file
       parameters/ vdw.parms.amb ; VDW parameter file
       box.pdb ; box pdb file
       0.4 ; grid spacing in angstroms
       1.4 ; probe radius for SA
       2 ; scoring type: SA
       8.0 ; cutoff for SA calculations
       output_prefix ; output grid prefix name

DESCRIPTION

The nchemgrid_gb and nchemgrid_sa programs create the GB and SA receptor grids for use with the Zou GB/SA scoring function (see Zou GB/SA Scoring). 

= OUTPUT FILES =

   For nchemgrid_gb
  • inva #debugging file with inverse Born radius for receptor atoms
  • NEG_INVA #error file listing embedded receptor atoms
  • OUTCHEM #restatement of input parameters; messages pertaining to calculation of the grids
  • OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
  • PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file

screen.para #file that contains descreening parameters

  • zou_grid.bmp #bump grid
  • zou_grid.rec #xyz coordinates, effective charge, effective vdw radii, inverse Born radii, and descreening parameters for receptor
  • zou_grid.sol #flags for whether receptor atoms are solvated
  • zou_grid.vdw #vdw values for receptor

For nchemgrid_sa:

  • OUTCHEM #restatement of input parameters; messages pertaining to calculation of the grids
  • OUTPARM #messages pertaining to parameterization of receptor atoms; net charge on the receptor molecule including any ions or waters in the receptor pdb file
  • PDBPARM #shows which parameters have been associated with each atom in the receptor pdb file
  • zou_grid.bmp #bump grid
  • zou_grid.sas #xyz coordinates, effective vdw radii, vdw type, number of spherical grid points, and polarity type for each receptor atom
  • zou_grid.sasmark #information about grid spacing, coordinates, dimensions, etc
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