VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sat Jun 06 2020 - 17:42:31 CDT

The way you are running the command is not correct.
Did you by any chance look at the volmap help guide?

See this.
http://www-s.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node153.html

This shows you how to set up the command - i.e. on the command line how
you pass arguments to volmap.

In the excerpt you have provided it appears you are trying to randomly
figure out what is missing. This is not recommended. You should always
carefully read the guide before using a command. Please see the above link
to find out how the command is being used and what arguments to provide.

If you are still stuck after that write back and someone will help.

On Sun, Jun 7, 2020 at 1:33 AM Muhammad tariq <tariqchemist112_at_gmail.com>
wrote:

> 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
>
> 

-- 
Best,
/A