> addIons: Argument #2 is type String must be of type: [unit]
Your addIons cmd is wrong. Try 'desc <ion_unit>' to see what you are
using, and 'list' to see all the units that are available.
> WARNING: There is a bond of 7.224966 angstroms between:
> ------- .R<THR 304>.A<C 13> and .R<THR 305>.A<N 1>
> WARNING: There is a bond of 10.331638 angstroms between:
> ------- .R<VAL 1168>.A<C 15> and .R<ASP 1169>.A<N 1>
> WARNING: There is a bond of 25.906360 angstroms between:
> ------- .R<GLY 1182>.A<C 6> and .R<GLY 1183>.A<N 1>
Possibly you have multiple molecules in your pdb file without TER
cards between them?
> WARNING: There is a bond of 3.265214 angstroms between:
> ------- .R<F3S 1453>.A<S3 3> and .R<F3S 1453>.A<S4 4>
> WARNING: There is a bond of 3.432639 angstroms between:
> ------- .R<F3S 1453>.A<S2 2> and .R<F3S 1453>.A<S3 3>
Looks like you have some long bonds in your prep file - do these agree
with experiment?
> WARNING: The unperturbed charge of the unit: -8.000010 is not zero.
Maybe because addIons didn't work?
> Could not find bond parameter for: FE - FE
> Could not find bond parameter for: FE - FE
...
> Could not find angle parameter: FE - FE - FE
You have Fe-Fe bond(s). What does your current prep file look like?
> Could not find bond parameter for: S - FE
> Could not find angle parameter: S - S - FE
Params for S-Fe will be needed - find or derive some and add via a
frcmod file.
Bill
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Sep 17 2008 - 03:11:00 PDT
