Grid

The current version is 21 (we have also versions 19 and 20, but the licenses are outdated).
The files are located in /home/bio/Grid/21/Linux
The homepage of the program is http://www.moldiscovery.com. (the program can be freely downloaded from there), but you need to obtain a license for every computer on which you will run the program.
An online manual is available in http://www.moldiscovery.com/docs/grid21/index.html.
The same files are locally available in /home/bio/Grid/21/Linux/manual/index.htm.
This manual also contains six tutorials that is strongly recommended for new users. The corresponding files are in /home/bio/Grid/21/Linux/tutorials/Tutorial01, a.s.o. See http://www.moldiscovery.com/docs/grid21/tutorials.html.
To run the programs, you have to add /home/bio/Grid/21/Linux/ to your path:
export PATH=/home/bio/Grid/21/Linux:$PATH
Yet, the grid program must be used with the full path (otherwise the licence file is not found):
/home/bio/Grid/grid/21/Linux

How to start a calculation

  1. Start with a coordinate file.

    2.  
  2. Run program great (to set up and run the grin calculation).
    1. 1 (grin)
    2. write a name for your job (all files will be named with this name.filetype); We will use the name protein in these instructions (note that the coordinate file must then be named protein.pdb).
    3. Give the absolute path to the grin program:

      4. 4
      /home/bio/Grid/21/Linux/grin
    4. Give the absolute path to the grub.dat file:

      5. 6
      /home/bio/Grid/21/Linux/grub.dat
    5. submit
    6. make a copy of the original coordinate file

      7. y
      new_file_name
    7. manage
    8. RETURN
    9. RETURN
    10. RETURN
    11. 7 (quit)

      12.  
  3. Alternatively (if you are an expert), you can run grin by the command

    4. grin <grin.in
     
  4. Check the output file protein.lout

    5. You can also inspect the protein.kout file, which is the actual output of the grin program, to be used of grid.
     
  5. Run program great again (to set up and run the actual grid calculation)
    1. 2 (grid)
    2. protein
    3. Give the absolute path to the grin program:

      4. 4
    4. submit
    5. Enter a title of the job
    6. 1
    7. RETURN
    8. 7 (quit)

      9.  
    In the main menu, you can optionally issue the command
    cage
    to define the box (e.g. using the command 1 (submit)
    or
    probe
    to define the probe (e.g. by 3 and then selecting the appropriate probe from one of the three submenues).
       
  6. The program has not created the grid.in file and then submitted the job using the command:

    7. grid <grid.in
    This may take several minutes if there is a large number of grid points.
     
  7. Study the result file protein.lont.

    8.  
  8. The actual result of the program is the protein.kont file. Study it with the gview program:

    9. gview protein.kont
    If you have done the tutorials, this is quite straight forward.


Notes


Possible probe molecules

 N3+   sp3 Amine NH3 cation             N2+   sp3 Amine NH2 cation
 N2:   sp3 NH2 with lone pair           N2=   sp2 Amine NH2 cation
 N2    Neutral flat NH2 eg amide        N1+   sp3 Amine NH cation
 N1:   sp3 NH with lone pair            N1=   sp2 Amine NH cation
 N1    Neutral flat NH eg amide         NH=   sp2 NH with lone pair
 N1#   sp NH with one hydrogen          N:    sp3 N with lone pair
 N:=   sp2 N with lone pair             N:#   sp N with lone pair
 N-:   Anionic tetrazole N              NM3   Trimethyl-ammonium cation
 O     sp2 carbonyl oxygen              O::   sp2 Carboxy oxygen atom
 O-    sp2 phenolate oxygen             O=    O of SO4 or sulfonamide
 OH    Phenol or carboxy OH             O1    Alkyl hydroxy OH group
 OC2   Ether oxygen                     OES   sp3 ester oxygen atom
 ON    Oxygen of nitro group            OS    O of sulfone / sulfoxide
 OH2   Water                            OFU   Furan oxygen atom
C3    Methyl CH3 group                 C1=   sp2 CH aromatic or vinyl
 PO4   PO4 phosphate dianion            PO4H  PO4H phosphate anion
 S1    Neutral SH group                 H     Neutral hydrogen atom
 F     Organic fluorine atom            F-    Fluoride anion
 CL    Organic chlorine atom            CL-   Chlorine anion
 BR    Organic bromine atom             BR-   Bromine anion
 I     Organic iodine atom              I-    Iodine anion
 LI+   Lithium cation                   NA+   Sodium cation
 K+    Potassium cation                 RB+   Rubidium cation
 CS+   Caesium cation                   MG+2  Magnesium cation
 CA+2  Calcium cation                   xxxx  Reserved for future use
 ZN+2  Zinc cation                      CU+2  Cupric copper cation
 FE+2  Ferrous iron cation              FE+3  Ferric iron cation
 BOTH  The amphipathic Probe            DRY   The hydrophobic Probe
 COO-                 Ionised alkyl carboxy group
 AR.COO-              Ionised aryl carboxy group
 CONH2                Alkyl amide
 AR.CONH2             Aryl amide
 CONHR              * Alkyl N-alkyl amide  R.CONHR
 AR.CONHR           * Aryl N-alkyl amide AR.CONHR
 AMIDINE              Alkyl amidine   R.C(NH2)2
 AR.AMIDINE           Aryl amidine   AR.C(NH2)2
 M-DIAMINE            meta-diamino-benzene