VMD-L Mailing List

From: Prathit Chatterjee (pc20apr_at_REMOVE_yahoo.co.in)
Date: Tue Jul 26 2022 - 08:50:27 CDT

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