[gmx-users] Software for PDB input for GROMACS

Thomas Piggot t.piggot at soton.ac.uk
Sat Nov 4 00:44:38 CET 2017

The nucleic acid builder should do what you want:




On 03/11/17 19:54, Dan Gil wrote:
> Hi,
> I would like to use the parmbsc1 force field to simulate DNA. I installed
> the force-field and am now actually running a simulation with a Drew
> Dickerson Dodecamer structure I downloaded from the RCSB database.
> Now I would like to generate my own structures and simulate them. I tried
> using Avogadro, but the software is not following the same conventions as
> parmbsc1 and therefore failing at pdb2gmx.
> Do you have recommendations on how to generate a PDB structure for nucleic
> acids? I suppose I could do this by hand, but I would very much like to
> avoid this path if I can.
> Best Regards,
> Dan

Dr Thomas Piggot
Visiting Fellow
University of Southampton, UK.

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