Hello all,
I want to do glycosaminoglycan (GAG) simulation in Gromacs. Initial structure and CHARMM topology for short chains can be obtained from Charmm GUI glycan modeler. But I have to take GAG chains of different arbitrary lengths for my project. Please do suggest a way to make structure and topology for arbitrarily long chain.
Thanks and regards.
Anirban Paul as GAGs are the polymer of repeating disaccharides you can easily draw the arbitrarily long chain structures using Chemdraw. You can also create your own topology files of different length GAGs using GROMACS.
Thank you.
Hello Md. Muzahid Ahmed Ezaj ,
Thank you so much for your suggestions. I used avogadro to build initial structure. But pdb2gmx did not work when I use it last time. I will check it again.
Thanks and regards,
Anirban
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