1. General topics
  3. Other
  5. Parameterizing a new molecule

normal Parameterizing a new molecule

  • ywang52
  • ywang52's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
7 years 9 months ago #5722 by ywang52
Parameterizing a new molecule was created by ywang52
Hi All

I am very new here. I am trying to run an amphiphilic polymer with MARTINI. As it is a new molecule, I am now learning to parameterize it first.

My question is, is that possible to generate the topology for the new molecule by "pbd2gmx" from an rtp file, or do I have to write the whole itp file for the molecule?

Thanks very much!

Yang

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

More
7 years 9 months ago #5723 by peterkroon
Replied by peterkroon on topic Parameterizing a new molecule
Hi and welcome :)

pdb2gmx can only help you with making atomistic topologies, as far as I know.
What you could try (since you have a polymer) is creating a coarse grained conformation (pdb), and feed that to pdb2gmx with an appropriate rtp, but there is a lot of dark magic in pdb2gmx, so I don't know if this will work.

See also: cgmartini.nl/index.php/tutorials-general...ng-new-molecule-gmx5

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

  • ywang52
  • ywang52's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
7 years 9 months ago #5742 by ywang52
Replied by ywang52 on topic Parameterizing a new molecule
Thank you! I agree with you, I wrote the itp by hand, and now it works.

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

  1. General topics
  3. Other
  5. Parameterizing a new molecule
Time to create page: 0.091 seconds