On Wed, Jan 23, 2013, Stefan Knippenberg wrote:
>
> Willing to solvate a system which has been running in production run for
> something like 100 ns, I got stuck by reading the pdb file in tleap:
>
> Created a new atom named: C165 within residue: .R<0 1>
You don't say how you made the pdb file.
> The pdb I started from is the final structure of a previous calculation,
> and reads like
>
> ATOM 233 7C16 0 1 171.290 58.160 51.330 0.00 0.00
But no standard amino acids or nucleic acids have atoms names like the above,
and you have a residue named "0" (zero), rather than a real residue name. So,
you will have to correctly generate a pdb file (use ambpdb), and you will have
to load the topology library (.lib, .mol2 or similar file) for the
non-standard residue. It is not enough just to load the frcmod file.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 23 2013 - 11:00:03 PST
