1. General topics
  3. Tools
  5. Collagen parameters seq2itp.pl vs. martinize.py

normal Collagen parameters seq2itp.pl vs. martinize.py

  • toma0052
  • toma0052's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
12 years 2 months ago #918 by toma0052
Collagen parameters seq2itp.pl vs. martinize.py was created by toma0052
Hello, I have a collagen-like protein for which I am aiming to use the MARTINI collagen parameters from Gautieri et al. (2010). In using the seq2itp.pl script from the supporting information of the JCTC paper and the martinize.py script with the -collagen flag, I am getting different itp parameters. In particular, using the former the BB proline beads are of type C5 whereas they are Na in the latter. Similarly the BB glycine residues are type N0 using seq2itp.pl and type P5 using martinize.py. It seems that the seq2itp.pl parameters are correct judging by the collagen.itp file on the MARTINI website, but I am wondering if the seq2itp.pl script is fully correct given updates to the force field that may have occurred in the 2 years that the seq2itp script was written.

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

More
12 years 1 month ago #929 by tsjerk
Replied by tsjerk on topic Collagen parameters seq2itp.pl vs. martinize.py
I'm not sure where the discrepancy comes from. I would say that martinize should reproduce the parameters from Gautieri. I will fix this. You can easily modify the parameters in your local copy of martinize.py. It's in the parameter tables, with secondary structure desgination 'F'. Thanks for reporting.

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

  • toma0052
  • toma0052's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
12 years 1 month ago #931 by toma0052
Replied by toma0052 on topic Collagen parameters seq2itp.pl vs. martinize.py
Thank you for the reply. Changing the BB bead types proved to be a easy fix, but I have noticed one other issue. It seems that when using martinize.py with the -collagen flag, the triple-helix specific dihedrals are not written to the *.itp file. The dihedrals are in the parameter tables and are correct, but I haven't been able to track down why they do not get written to the output itp.

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

More
11 years 11 months ago #939 by xavier
Replied by xavier on topic Collagen parameters seq2itp.pl vs. martinize.py

toma0052 wrote: Thank you for the reply. Changing the BB bead types proved to be a easy fix, but I have noticed one other issue. It seems that when using martinize.py with the -collagen flag, the triple-helix specific dihedrals are not written to the *.itp file. The dihedrals are in the parameter tables and are correct, but I haven't been able to track down why they do not get written to the output itp.


We've had a problem with the server and have not been notified of reaction on the forum. Our apologizes for that.

We were wandering if you had find a solution for the problem?

XAvier.

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

  • toma0052
  • toma0052's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
11 years 11 months ago #953 by toma0052
Replied by toma0052 on topic Collagen parameters seq2itp.pl vs. martinize.py
Using the old seq2itp.pl script from Gautieri et al. backbone dihedrals specific to the collagen triple helix were written to the topology file. Using the martinize.py script with the -collagen flag, no triple helix specific backbone dihedrals are written to the itp file, only sidechain improper dihedrals are written. For the time being, I had been using the old script.

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

More
11 years 11 months ago #954 by xavier
Replied by xavier on topic Collagen parameters seq2itp.pl vs. martinize.py
Tks for reporting. Djurre is heavily sweating on (fixing) it.

toma0052 wrote: Using the old seq2itp.pl script from Gautieri et al. backbone dihedrals specific to the collagen triple helix were written to the topology file. Using the martinize.py script with the -collagen flag, no triple helix specific backbone dihedrals are written to the itp file, only sidechain improper dihedrals are written. For the time being, I had been using the old script.

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

More
11 years 10 months ago #975 by djurre
Replied by djurre on topic Collagen parameters seq2itp.pl vs. martinize.py
For completeness: It took slightly longer then planned, but there is a new martinize version (1.2) with correct collagen parameters.

Thanks a lot for reporting!

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

  1. General topics
  3. Tools
  5. Collagen parameters seq2itp.pl vs. martinize.py
Time to create page: 0.097 seconds