normal Covalently link glycan (NAG) groups to a protein

  • siladitya.padhi
  • siladitya.padhi's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 months 3 weeks ago #8619 by siladitya.padhi
Covalently link glycan (NAG) groups to a protein was created by siladitya.padhi
I am trying to covalently link N-acetyl-glucosamine (NAG) groups to asparagine residues in a protein. The protein is already in a MARTINI format (with GRO and ITP files). I have taken the MARTINI parameters for NAG bound to asparagine from a recently published preprint, and defined NAG-asparagine as a residue in the martini_v2.2_aminoacids.itp file. However, when I run pdb2gmx for generating the ITP file for the protein with NAG groups, it complains about a missing RTP file in the MARTINI force field directory. I could not find any RTP file for the MARTINI force field. Is there any other way to generate an ITP file for the protein with the NAG groups?

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

  • peterkroon
  • peterkroon's Avatar
  • Away
  • Gold Boarder
More
2 months 3 weeks ago #8622 by peterkroon
Replied by peterkroon on topic Covalently link glycan (NAG) groups to a protein
Hi,

you can't use pdb2gmx to prepare Martini files starting from atomistic structures, which is why there's no rtp files for Martini. In addition, pdb2gmx won't be able to make non-linear polymers (because your NAG addition is a branch on the protein).

Solutions:
1) if you only need to do this once, do it by hand.
2) if you need to do this multiple times, and/or you're feeling adventurous, take a look at Martinize2 ( github.com/marrink-lab/vermouth-martinize ), which should be capable of generating the input files you need starting from an atomistic pdb. Unfortunately there is not much available in way of documentation and tutorials at the moment, so you'll have to figure out the how and what by looking at the provided files (vermouth/data directory). In addition, check the produced itp carefully.

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

  • siladitya.padhi
  • siladitya.padhi's Avatar Topic Author
  • Offline
  • Fresh Boarder
More
2 months 3 weeks ago #8625 by siladitya.padhi
Replied by siladitya.padhi on topic Covalently link glycan (NAG) groups to a protein
Thank you for your response, Peter! I prepared the ITP file by hand, as you had suggested.

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

Time to create page: 0.086 seconds