Hi, everyone
Recently, I want to create polymer of all-atomic model (e.g. PAMAM). Now I have a PDB file about the monomer (amidoamine). How can I use VMD or Xplor to generate polymer of amidoamine?
Best Regards,
Shen
Hi!
May be this can help you:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/0518.html
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2013-2014/0622.html
http://towhee.sourceforge.net/algorithm/polymer.html
http://lammps.sandia.gov/tutorials/italy14/VMD_Visualization_Scripting_TopoTools.pdf
Kirill,
Thank you for your help! These websites are very useful for me.
However, I just have CHARMM format topology file about mononer. Can I use the mononer topology file in polymer pdb file?
Good luck!
Shen
Not exactly what you asked for, but please check,
https://www.researchgate.net/publication/257369991_Polymatic_A_generalized_simulated_polymerization_algorithm_for_amorphous_polymers
for a good option for polymerization applications using a free software(LAMMPS in this case.). Also Packmol package of LAMMPS can be used to create a initial box to be used.
Article Polymatic: A generalized simulated polymerization algorithm ...
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