On Tue, Aug 17, 2010, Jorgen Simonsen wrote:
>
> I just reinstalled ambertools - ambertool11 and generated a pdbfile from a
> small minimization
>
> ambpdb -p new.prmtop < min.rst > min.pdb
>
> when I load the new pdbfile into xleap I get the following
>
> Created a new atom named: H within residue: .R<NASP 1>
Well....what is in "min.pdb"?? Is there an H atom in residue 1? If so, how
did it get there? (Probably was in new.prmtop). This suggests that you
created "new.prmtop" in some way that is different from what you are doing
now.
>
> and furthermore some hydrogen water residues are unrecognized
>
> Created a new atom named: H within residue: .R<WAT 1517>
Same questions, which are the ones you should be asking yourself. Learning to
debug problems is an important part of learning to use Amber (and indeed,
other programs.)
....dac
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Received on Tue Aug 17 2010 - 08:00:03 PDT
