Dear Dr. Thomas Steinbrecher
Since I'm beginner in amber, and I used pdb files without change,
please explain this way by example or tutorial.
Thanks in advance.
On Sun, Feb 19, 2012 at 6:33 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > As you said, if I build a single pdb-file of my system with water and
> > ions,
> >
> > how to change GC base pair to AT?
>
> you could build a fully solvated DNA with GC basepair, then rename the
> TI-involved residues A and T and remove or rename all atoms as
> appropriate. leap will automatically add all that is missing when you
> reload the pdb. This is not the only way to build input structures for TI,
> but has often worked fine for me.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Sun Feb 19 2012 - 08:00:02 PST
