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AMBER Archive (2004)Subject: Re: AMBER: Bond type in leap
From: Bill Ross (ross_at_cgl.ucsf.edu)
> when i load the saved pdb files in leap and use desc to get the
The bond order is only used when leap minimizes and there are no regular
> Initially when I loaded the peptide in leap it added 4 missing atoms:
This implies that leap may have converted a terminal residue to the amber
> Added missing heavy atom: .R<CGLN 10>.A<OXT 18>
The main problem here is leap adding an unrecognized atom from the pdb:
> Created a new atom named: H within residue: .R<NGLN 1>
This could be because of an atom naming difference. The simplest approach
Bill
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