Author Topic: joining coord files  (Read 1539 times)

ym21d@fsu.edu

  • Jr. Member
  • **
  • Posts: 10
  • Karma: +0/-0
joining coord files
« on: May 24, 2024, 08:33:22 PM »
Hello,

I am trying to use woelfling-job, but I am not sure the correct way of combining my coord files into a file called coords. Do you have any idea? If so, could you email me at ym21d@fsu.edu

Thank you,
Yael

antti_karttunen

  • Sr. Member
  • ****
  • Posts: 229
  • Karma: +1/-0
Re: joining coord files
« Reply #1 on: May 26, 2024, 05:25:22 PM »
Hi, here is a short practical tutorial into the use of woelfling: https://wiki.aalto.fi/display/IMM/Searching+for+transition+states.

Best wishes,
Antti

ym21d@fsu.edu

  • Jr. Member
  • **
  • Posts: 10
  • Karma: +0/-0
Re: joining coord files
« Reply #2 on: June 04, 2024, 07:46:11 PM »
Thank you Antti,

That is very helpful. I Have another question. If my starting and ending structures don't have the same atom numbering, is there a way of changing the atom numbering. I have done it by moving lines in the xyz file, but that may not be practical with a molecule with 38 atoms or more.

Thank you,
yael

antti_karttunen

  • Sr. Member
  • ****
  • Posts: 229
  • Karma: +1/-0
Re: joining coord files
« Reply #3 on: June 04, 2024, 09:32:02 PM »
Hi,

adjusting the atom numbering is pretty much manual work. Ot maybe someone has created a Python script that would do it, but I'm not aware of any. I suggest using a graphical visualization program like TMoleX, Avogadro, Chemcraft or Gaussview to renumber the atoms.

Best,
Antti