On Mon, Dec 15, 2014, Anupam Goel wrote:
> I have been trying to run amber with a peptide conjugated with unsual ADP-ribose attachment and keep getting this error whatever I try. Any suggestions?
>
> > saveamberparm 15aa_APR 15aa_APR.prmtop 15aa_APR.inpcrd
> Checking Unit.
> ERROR: The unperturbed charge of the unit: 0.097100 is not integral.
> WARNING: The unperturbed charge of the unit: 0.097100 is not zero.
> ERROR: The perturbed charge: 0.097100 is not integral.
> WARNING: The perturbed charge: 0.097100 is not zero.
>
> -- ignoring the errors and warnings.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: O2 - C3
> Could not find bond parameter for: CD - NA
...
We need more information: how did you make the library file for the modified
peptide? What force fields did you load into leap? Amber doesn't have any
atom types (in its standard protein and nucleic acid force fields) named "C3",
so it is not surprising that there are no parameters for this. How did you
assign atom types?
....dac
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Received on Mon Dec 15 2014 - 18:00:03 PST
