VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jul 26 2022 - 12:09:13 CDT

To be able to write files in a specific format, the corresponding molfile
plugin must support writing. However the plugin for .cor files has only
read but not write support.

On Tue, Jul 26, 2022 at 1:03 PM Prathit Chatterjee <
pc20apr_at_remove_yahoo.co.in> wrote:

> Dear VMD Experts,
>
> I wanted to know whether there is any specific way to write CHARMM cor
> files with VMD, from psf and pdb/dcd/nc files.
>
> I tried the trivial one guessable, but could not succeed, as follows:
>
> vmd > mol new step3_input.psf
>
> psfplugin) Detected a Charmm PSF file
>
> psfplugin) Detected a Charmm PSF EXTEnded file
>
> Info) Using plugin psf for structure file step3_input.psf
>
> Info) Analyzing structure ...
>
> Info) Atoms: 1394424
>
> Info) Bonds: 1391839
>
> Info) Angles: 472555 Dihedrals: 15449 Impropers: 1094 Cross-terms:
> 350
>
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
>
> Info) Residues: 465000
>
> Info) Waters: 462002
>
> Info) Segments: 4
>
> Info) Fragments: 464648 Protein: 2 Nucleic: 0
>
> 0
>
> vmd > mol addfile step5_4.nc_frame2.pdb
>
> Info) Using plugin pdb for coordinates from file step5_4.nc_frame2.pdb
>
> 0
>
> Info) Finished with coordinate file step5_4.nc_frame2.pdb.
>
> vmd >
>
> vmd >
>
> vmd > set all [atomselect top all]
>
> atomselect0
>
> vmd > $all writecor step5_4.nc_frame2.cor
>
> ERROR) Unable to open file step5_4.nc_frame2.cor of type cor for writing
> frames.
>
> vmd > $all writecor step5_4.nc_frame2.cor type cor
>
> atomselection: improper method: writecor
>
> usage: <atomselection> <command> [args...]
>
>
> Commands for manipulating atomselection metadata:
>
> frame [new frame value] -- get/set frame
>
> molid|molindex -- get selection's molecule id
>
> text -- get selection's text
>
> delete -- delete atomselection (to free memory)
>
> global -- move atomselection to global scope
>
> update -- recalculate selection
>
>
> Commands for getting/setting attributes:
>
> num -- number of atoms
>
> list -- get atom indices
>
> get <list of attributes> -- for attributes use 'atomselect keywords'
>
> set <list of attributes> <nested list of values>
>
> getbonds -- get list of bonded atoms
>
> setbonds <bondlists>
>
> getbondorders -- get list of bond orders
>
> setbondorders <bondlists>
>
> getbondtypes -- get list of bond types
>
> setbondtypes <bondlists>
>
> moveto|moveby <3 vector> -- change atomic coordinates
>
> lmoveto|lmoveby <x> <y> <z>
>
> move <4x4 transforamtion matrix>
>
>
> Commands for writing to a file:
>
> writepdb <filename> -- write sel to PDB file
>
> writeXXX <filename> -- write sel to XXX file (if XXX is a
> known format)
>
>
> vmd > exit
>
> Info) VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020)
>
> Info) Exiting normally.
> (base) [Prathit_at_master
> ]~/APP/OnlyAPP/AlphaFold2/770_res/Charmm-Gui_Dimer-units/E1-E2_75Aenm/charmm-gui-3765059778/amber>
>
> ============
>
> Any comments and suggestions will be deeply appreciated.
>
> Thank you,
> Regards,
> Prathit
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!7eO6P9ZZwMIs8dqOXyjeNwAsrpEluGpVN-24uK0zr2QB03HgrA-V-LZfslpHOv8AEBl-vbufv5WR-nMxvg$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.