Re: [AMBER] help: MD on DNA

From: Jason Swails <>
Date: Fri, 3 Oct 2014 12:23:37 -0400

On Oct 3, 2014, at 10:15 AM, pradeep pant <> wrote:

> Hi,
> Can anyone please tell me what steps should I take to create prmtop and crd
> file of a DNA.
> I am not getting how to create these files even after learning it from
> AMBER tutorial.

The steps are outlined in the tutorial. Theres nothing different that we would tell you that the tutorial does not tell you (otherwise we would change the tutorial to say the correct process instead).

> Whatever DNA pdb I am using it is showing some atoms are not in the residue
> templates whem I am loading the pdb using tleap. H atoms are added byTleap
> but missing residue template problem is still there.

This is, at the end of the day, a problem with your input DNA PDB file, not a problem with the process of creating a prmtop outlined in the Amber tutorials. The choice for the atom names of the various DNA residues is somewhat arbitrary. We [1] felt that the best choice (i.e., the choice that would cause the fewest problems) is to adopt the same naming scheme used by the PDB for those residues. What this means is that for most PDBs that you download from the PDB website, those files will work in tleap with little to no modifications.

What this means, though, is that any place that you download a PDB file that does NOT use the same residue and atom naming scheme as the PDB may require a lot of modifications to get it to work in tleap.

So if you cant get the source of your PDB file to print out more PDB-like names for the atoms, then you will have to sit down with your PDB file and the residue templates ($AMBERHOME/dat/leap/lib/nucleic12.lib) and make sure each of the atom names in your PDB matches the corresponding atom in the residue template. If its only a small number of atoms that change, you can try deleting those atoms and having tleap add them back (leap will add _any_ missing atom, not just hydrogens). However, the more atoms that leap has to fill in, the higher chance you will have that the starting structure will have problems.

I hope this helps, and good luck.

[1] This choice was made long ago, way before I was part of We, but I still think its the best choice.

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 03 2014 - 09:30:02 PDT
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