The original PDB files downloaded from PDB.org without HXT. We have used
schrodinger suite to rebuild the miss amino acids and exported as pdb files
to further simulation.
Yes, these two residues are C-terminal residues. Could I just delete these
HXT lines for the simulation?
Thanks a lot
2017-09-13 21:27 GMT+08:00 David A Case <david.case.rutgers.edu>:
> On Wed, Sep 13, 2017, jacky zhao wrote:
>
> > Loading PDB file: ./wt_for_simulation.pdb
> > Created a new atom named: HXT within residue: .R<CALA 115>
> > Created a new atom named: HXT within residue: .R<CGLU 229>
>
> You have atoms named HXT in residues 115 and 229. These are not part of
> any
> Amber residue libraries, so tleap doesn't know what to do with them.
>
> In a separate email, you say that you deleted these atoms and continued
> the simulation. That's likely to be the right thing to do, but you should
> try to see why those atoms came up in the first place. Do you perhaps
> require
> a neutral C-terminal residue?
>
> ....dac
>
>
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--
Lei Zhao, Ph.D.
International Joint Cancer Institute of the Second Military Medical
University
National Engineering Research Center for Antibody Medicine
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Received on Wed Sep 13 2017 - 07:00:03 PDT
