On Wed, Jun 27, 2012, Brandon Sim wrote:
>
> A PDB file I am working on has several missing residues, so I added them in
> manually by copying and pasting the residue info in from another similar
> PDB file that does have those residues. However, as expected, the bond
> lengths between these residues is a bit off (~4 angstroms).
>
> I was hoping that sander would just snap these bonds back into place during
> minimization and would fix the problem. However, when I am preparing the
> inpcrd and parmtop files through tleap, it keeps thinking that because of
> the long distance between the atoms mentioned before, the two belong to
> separate molecules; hence, tleap adds in HXT to the end of the preceding
> residue.
Something else must be going on: tleap doesn't take such actions based on
bond distances, as far as I know. In particular, Amber libraries don't
have any atoms named "HXT". So we would need to know details about exactly
what you are doing--can you make a small example that exhibits the behavior
you describe?
....dac
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Received on Wed Jun 27 2012 - 13:00:02 PDT
