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 - 12:30:02 PDT
