On Fri, Apr 23, 2010, Bill Ross wrote:
> > I am a freshman on AMber and I am running the Tutorial on loop dynamics of
> > HIV-1 integrase core domain. There is something wrong when I tried to run
> > saveAmberParm.
> >
> > > source leaprc.ff03
> > > mol=loadpdb wt1mg_water.pdb
> > Loading PDB file: ./wt1mg_water.pdb
> > -- residue 1: duplicate [2H] atoms (total 2)
> > Warning: Atom names in each residue should be unique.
> > (Same-name atoms are handled by using the first
> > occurrence and by ignoring the rest.
> > Frequently duplicate atom names stem from alternate
> > conformations in the PDB file.)
> > Unknown residue: MG number: 154 type: Terminal/last
It's not clear how you created the "wt1mg_water.pdb" file, but it is easy
enough to examine it to see if there are duplicate H atoms in residue 1. They
probably won't cause any problem.
The "Unknown residue: MG" message is discussed in the tutorial, which
deliberately arranged for that message to be issued, so that users could learn
how to recover from common problems.
...hope this helps....dac
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Received on Fri Apr 23 2010 - 11:00:02 PDT
