AMBER Archive (2009)
Subject: Re: [AMBER] (no subject)
From: case (case_at_biomaps.rutgers.edu)
Date: Fri Aug 07 2009 - 18:54:18 CDT
On Fri, Aug 07, 2009, Ross Walker wrote:
> It looks like the hydrogen naming for LEU residue 1 in your pdb file does
> not follow the format for terminal residues correctly. Quick fix is to
> remove all the H's from this residue and then let Leap add them back in.
Ross' workaround is OK, but this looks like a bug in tleap(?). The hydrogen
naming for your terminal residue is indeed correct for the old (pdb version 2)
pdb format. I don't know whether this will get fixed, since I think we
now do the "right thing" for pdb format 3 files.
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