Re: [AMBER] problem on running saveAmberParm

From: Bill Ross <>
Date: Fri, 23 Apr 2010 10:27:27 -0700 (PDT)

> 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.
> The program reads:
> > 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

This is surprising for a tutorial - there should be no
duplicate atoms for a residue in the pdb. Were there any
instructions in the tutorial about deleting one? Also I
would expect the tutorial to load the definition for the
MG residue. These are more like problems that a newcomer
sees with their new setup than I would expect in a tutorial.
Did you miss any steps?


AMBER mailing list
Received on Fri Apr 23 2010 - 10:30:04 PDT
Custom Search