1. The site is back up. We will have a new site on a new, more
robust, server very soon (by end of January or earlier, if all goes
well). Sorry for any inconvenience. In the meantime, just write me
off-list if it's down.
2. I don't know enough detail to be sure, but it looks as if you
changed atom types within your amino acids to be GLYCAM-06h types. If
you have done that, then undo it . The amino acid atom types should
be appropriate to the protein force field. Also, depending on the
glycan, you might need the 06h-1 parameters available at the site
above (if you want to use 12SB, also get the amino acid files and
leaprc). If you didn't do that, then I need more information before I
can help. In particular, what type of residue contains these bonds
and angles?
On Fri, Dec 14, 2012 at 12:03 PM, Urszula Uciechowska
<urszula.uciechowska.chem.umu.se> wrote:
> Dear AMBER users,
>
> I am trying to adopt the atom types for the glycam_06h. I fallowed the glycam.dat file and changed the atom types but I am still getting an error,
>
>
> Could not find bond parameter for: CT - Hp
> Could not find bond parameter for: CT - Hp
> Could not find bond parameter for: CT - Hc
> Could not find bond parameter for: CT - Hc
> Could not find bond parameter for: CT - Hc
> Could not find bond parameter for: CT - Hc
> Checking for angle parameters.
> Could not find angle parameter: Hp - CT - N3
> Could not find angle parameter: Hp - CT - Hp
> Could not find angle parameter: Hp - CT - N3
> Could not find angle parameter: CT - CT - Hp
> Could not find angle parameter: CT - CT - Hp
> Could not find angle parameter: Hc - CT - CT
> Could not find angle parameter: Hc - CT - Hc
> Could not find angle parameter: Hc - CT - CT
> Could not find angle parameter: Hc - CT - CT
> Could not find angle parameter: Hc - CT - Hc
> Could not find angle parameter: Hc - CT - CT
> Could not find angle parameter: CT - CT - Hc
> Could not find angle parameter: CT - CT - Hc
> Could not find angle parameter: CT - CT - Hc
> Could not find angle parameter: CT - CT - Hc
>
> Should I change CT to C?
>
> best regards
> Urszula
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 14 2012 - 10:00:02 PST
