VMD-L Mailing List

From: Parth Chaturvedi (parth9022_at_gmail.com)
Date: Mon Jul 01 2019 - 18:34:51 CDT

Dear users,

I am trying to simulate a protein-dna complex using martini forcefield. Is
there a .cgc file for DNA which I can use in CG builder of VMD to build the
necessary pdb and psf files if not then how can I prepare one?

Also, are there parameter files for DNA which I will be needing to run NAMD
simulation and if not then how can I build one?

Currently, the tutorial for DNA from martini website only works for GROMACS
simulations while the martini tutorial for NAMD does not include any DNA
structures.

Best regards,
Parth