1. General topics
  3. Tools
  5. Error in the FG topology generation of Backward

normal Error in the FG topology generation of Backward

  • falcon40phoenix
  • falcon40phoenix's Avatar Topic Author
  • Visitor
9 years 4 months ago #4257 by falcon40phoenix
Error in the FG topology generation of Backward was created by falcon40phoenix
After correctly generating the topology from FG to CG using martini.py an MD has been conducted (after minim equilibration) for a protein in water solution.
the generated dynamic.gro is used to generate and FG topology using pdb2gmx but an error occured :


Program pdb2gmx, VERSION 4.6.5
Source code file: /home/phoenix/Downloads/gromacs-4.6.5/src/kernel/hizzie.c, line: 346
Fatal error:
Incomplete ring in HIS34

dynamic.gro contain this lines about HIS34
34HIS BB 77 10.660 3.286 9.036 -0.3379 0.1513 -0.1003
34HIS SC1 78 10.853 3.032 8.998 -0.2862 -0.1189 0.1952
34HIS SC2 79 11.042 2.937 9.166 0.0381 0.1110 -0.0277
34HIS SC3 80 10.940 2.777 8.975 0.1434 0.0376 -0.0234

I can't find the source of error please help

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

More
9 years 1 month ago #4486 by Clement
Replied by Clement on topic Error in the FG topology generation of Backward
You're feeding a CG structure (look at the bead names) where you'd need to provide a FG one (hence the "incomplete ring" error).

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

  1. General topics
  3. Tools
  5. Error in the FG topology generation of Backward
Time to create page: 0.086 seconds