note: they both have +1 charge.
On Wed, Jun 27, 2012 at 3:09 PM, Brandon Sim <simpavid.gmail.com> wrote:
> Dear all,
>
> 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.
>
> Is there a way I can stop tleap from doing this?
>
> Thanks,
> Brandon
>
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Received on Wed Jun 27 2012 - 12:30:03 PDT
