Thank you for the suggestion, David.
There were two gotchas that other's might hit, just like I did:
1. don't forget to delete the H5 atom in your pdb file
2. in order to make the parameters compatible with the amber99SBildn
force field, I had to change the atom type for the C5' atom to CT
On Wed, Mar 12, 2014 at 12:33 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Mar 12, 2014, Sidney Elmer wrote:
>
> > This information was very helpful. I would like to build double
> > stranded DNA with methylated cytosines directly in NAB using bdna().
> > I looked through the NAB code and quickly got lost. I'm happy to do
> > this myself, but I would appreciate some guidance as to how to do
> > this. Could someone please outline the steps necessary to accomplish
> > this? Thank you!
>
> First, use NAB to build a standard BNDA helix [use fd_helix(), not bdna()].
> See tutorial B1 for a detailed walk-through on how to do this.
> An easier alternative for most cases is to visit w3dna.rutgers.edu.
>
> Second, edit the PDB file to change the DC residue names to whatever your
> library is calling methylated cytosine; let LEaP build the structure from
> the un-methylated structure.
>
> ...good luck...dac
>
>
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Received on Wed Mar 12 2014 - 17:30:03 PDT
