Hi I m trying to build an initial starting pdb structure of a dna molecule for OPLS/AA based MD simulation. I was trying to use the link "http://web.x3dna.org/custom/buildcomb" for building and I found that the output pdb does not model the 5' and 3' terminal residues and also none of the residues carries hydrogen. How can I solve this. Where can we build DNAs with hydrogen added?
dear shakkira,
try chimera 1.14 to build DNA structure
like this figure and you can convert to pdb file
Noer Komari But I have seen that chimera does not give you an initial starting structure for the simulations.
Dear Shakkira Erimban
You can use Schrodinger's Maestro (3D builder) to build the 3D structure of the DNA and export it into .pdb for your further analysis.
Shaban Ahmad
Hi Shaban
Is this a paid software ? I could not see a direct download online. Can you share the link for downloading.
Yes Schrodinger is paid but you van get trial licence also Maestro visualiser is free for all.
You need to have a account for free download
https://www.schrodinger.com/downloads/releases
Shaban Ahmad Have you ever performed MD simulations of DNA systems with Gromacs?
No, I did for Protein-ligand complex using gromacs, NAMD and Desmond too.
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