Whoops - upon checking the PDB file in more detail, it appears that 'HXT'
was a file type that was already in the input PDB I obtained from the
online database. Not AMBER's fault at all -- sorry.
Will sander be able to snap the bond back to its equilibrium length?
Thanks,
Brandon
On Wed, Jun 27, 2012 at 3:51 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 - 13:30:03 PDT
