Dear Lachele,
I attached you my molecule. Firstly I load:
source leaprc.ff99SB
then I load source leaprc.GLYCAM_06h.
I am not sure anymore if this is the right procedure ...
I am trying to use AMBER12 with AMBER 11 and glycam_06g worked fine...
Thank you in advance for your help
/Urszula
________________________________________
Von: Lachele Foley (Lists) [lf.list.gmail.com]
Gesendet: Freitag, 14. Dezember 2012 18:35
An: AMBER Mailing List
Betreff: Re: [AMBER] glycam_06h atom types
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
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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- application/octet-stream attachment: test.mol2
Received on Fri Dec 14 2012 - 10:00:03 PST
