VMD-L Mailing List

From: Prathit Chatterjee (pc20apr_at_REMOVE_yahoo.co.in)
Date: Thu Jul 14 2022 - 08:54:37 CDT

Dear VMD experts,

Kindly please let me know how to write parm7 file with VMD, from a previous pdb and parm7 file.
I am using VMD for LINUXAMD64, version 1.9.4a51 (December 21, 2020).

vmd > $a writeparm7 init_0.15IC_noW.parm7 type parm7

atomselection: improper method: writeparm7

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)
Awaiting your feedback,

Regards,Prathit