normal Viewing MARTINI models with CONECT records

  • darrenphua
  • darrenphua's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
4 years 1 week ago #8644 by darrenphua
Viewing MARTINI models with CONECT records was created by darrenphua
I am aware that using gmx trjconv once mdrun is completed would be able to show martini models with connecting bonds. This is done by input of -conect.

However, if i want to view the connecting bonds in a martini model immediately after converting the all-atom model to martini, can this be done using gmx editconf? I see from the documentation that editconf has a -conect option, but i received this error in doing so.

Assertion failed:
Condition: fio->xdr != nullptr
Implementation error: NULL XDR pointers


The command line i input is this:
gmx editconf -f protein-CG.pdb -o protein-CG-conect.pdb -conect

Please Log in or Create an account to join the conversation.

More
3 years 11 months ago #8656 by peterkroon
Replied by peterkroon on topic Viewing MARTINI models with CONECT records
You need to give editconf a tpr file, since that contains the necessary information. You can create a minimization tpr (without actually running the minimization) for this purpose.

Please Log in or Create an account to join the conversation.

Time to create page: 0.097 seconds