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 - 07:30:01 PST
