VMD-L Mailing List

From: Muhammad tariq (tariqchemist112_at_gmail.com)
Date: Sat Jun 06 2020 - 12:08:27 CDT

Hi Developers,
i am trying to compute the volmap of my biological system but could not
find out.
The following commands are pasted below take a look and suggest to me where
i am making mistakes. I will be grateful to you. thanks

Main console display active (Tcl8.5.6 / Tk8.5.6)
(amber_format) 1 % package require ilstools
1.5
>Main< (amber_format) 2 % volmap
usage: volmap <command> <args...>

Volmap Creation:
 volmap <maptype> <selection> [opts...] -- create a new volmap file
 maptypes:
   density -- arbitrary-weight density map [atoms/A^3]
   interp -- arbitrary-weight interpolation map [atoms/A^3]
   distance -- distance nearest atom surface [A]
   occupancy -- percent atomic occupancy of gridpoints [%]
   mask -- binary mask by painting spheres around atoms
   coulomb -- Coulomb electrostatic potential [kT/e] (slow)
   coulombmsm -- Coulomb electrostatic potential [kT/e] (fast)
   ils -- free energy map [kT] computed by implicit ligand sampling
 options common to all maptypes:
   -o <filename> -- output DX format file name (use .dx extension)
   -mol <molid> -- export volmap into the specified mol
   -res <float> -- resolution in A of smallest cube
   -allframes -- compute for all frames of the trajectory
   -combine <arg> -- rule for combining the different frames
                              <arg> = avg, min, max, stdev or pmf
   -minmax <list of 2 vectors> -- specify boundary of output grid
 options specific to certain maptypes:
   -points -- use point particles for occupancy
   -cutoff <float> -- distance cutoff for calculations [A]
   -radscale <float> -- premultiply all atomic radii by a factor
   -weight <str/list> -- per atom weights for calculation
 options for ils:
   see documentation

>Main< (amber_format) 3 % volmap ils all
wrong # args: should be "volmap ils <molid> <minmax> [options...]"
>Main< (amber_format) 4 % volmap ils top all
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected.volmap ils: No probe VDW parameters specified.
>Main< (amber_format) 5 % volmap ils top all 23 23
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected. volmap ils: unknown argument 23
>Main< (amber_format) 6 % set all [atomselect top all]
atomselect0
>Main< (amber_format) 7 % measure minmax $all
{-12.547986030578613 -11.045787811279297 -10.894913673400879}
{94.13382720947266 97.49641418457031 91.94561004638672}
>Main< (amber_format) 8 % volmap ils $all pbc wrap
expected integer but got "atomselect0"volmap: molecule specified for ouput
is invalid. (-mol)
>Main< (amber_format) 9 % volmap ils oxygen pbc wrap
expected integer but got "oxygen"volmap: molecule specified for ouput is
invalid. (-mol)
>Main< (amber_format) 10 % volmap ils complex_cyy.pdb pbc wrap
expected integer but got "complex_cyy.pdb"volmap: molecule specified for
ouput is invalid. (-mol)
>Main< (amber_format) 11 % volmap ils -mol pbc wrap
expected integer but got "-mol"volmap: molecule specified for ouput is
invalid. (-mol)
>Main< (amber_format) 12 % volmap ils pbc wrap
expected integer but got "pbc"volmap: molecule specified for ouput is
invalid. (-mol)
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 %
>Main< (amber_format) 13 % volmap ils complex_cyy.pdb pbc wrap
expected integer but got "complex_cyy.pdb"volmap: molecule specified for
ouput is invalid. (-mol)
>Main< (amber_format) 14 %
>Main< (amber_format) 14 %
>Main< (amber_format) 14 % pbc get
{82.036125 82.036125 82.036125 90.000000 90.000000 90.000000}
>Main< (amber_format) 15 % volmap density [atomselect top "all"] -res 1.0
CHECKPOINTNAME = checkpoint:density_out.dx
>Main< (amber_format) 16 % volmap ils [atomselect top "all"] -res 1.0
expected integer but got "atomselect2"volmap: molecule specified for ouput
is invalid. (-mol)
>Main< (amber_format) 17 % volmap density [atomselect top "all"] -res 1.0
volmap: no atoms selected.
>Main< (amber_format) 18 % volmap ils [atomselect top "all"] -res 1.0
expected integer but got "atomselect4"volmap: molecule specified for ouput
is invalid. (-mol)
>Main< (amber_format) 19 % volmap ils [atomselect top "all"]
wrong # args: should be "volmap ils <molid> <minmax> [options...]"
>Main< (amber_format) 20 % volmap ils [atomselect top "all"] pbc wrap
expected integer but got "atomselect6"volmap: molecule specified for ouput
is invalid. (-mol)
>Main< (amber_format) 21 % set sel [atomselect top "water"]
atomselect325
>Main< (amber_format) 22 % set sel [atomselect top "water"]
atomselect326
>Main< (amber_format) 23 % $sel text
water
>Main< (amber_format) 24 %
>Main< (amber_format) 24 %
>Main< (amber_format) 24 % volmap ils $sel pbc wrap
expected integer but got "atomselect326"volmap: molecule specified for
ouput is invalid. (-mol)
>Main< (amber_format) 25 %
>Main< (amber_format) 25 %
>Main< (amber_format) 25 % volmap ils 0 pbc wrap
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected. volmap ils: unknown argument wrap
>Main< (amber_format) 26 % volmap ils -mol 0 pbc wrap
expected integer but got "-mol"volmap: molecule specified for ouput is
invalid. (-mol)
>Main< (amber_format) 27 % volmap ils 326 pbc wrap
volmap: molecule specified for ouput is invalid. (-mol)
>Main< (amber_format) 28 % volmap ils 326 pbc wrap
volmap: molecule specified for ouput is invalid. (-mol)
>Main< (amber_format) 29 % molinfo top
1
>Main< (amber_format) 30 % volmap ils 1 pbc wrap
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected. volmap ils: unknown argument wrap
>Main< (amber_format) 31 % volmap ils 1 pbc
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected.volmap ils: No probe VDW parameters specified.
>Main< (amber_format) 32 % volmap ils 1
wrong # args: should be "volmap ils <molid> <minmax> [options...]"
>Main< (amber_format) 33 % volmap ils 1 -minmax
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected.volmap ils: No probe VDW parameters specified.
>Main< (amber_format) 34 % volmap ils 1 -minmax
volmap: minmax requires a list with two vectors (-minmax)volmap: no atoms
selected.volmap ils: No probe VDW parameters specified.
>Main< (amber_format) 35 %
>Main< (amber_format) 35 % volmap ils 1 -minmax