06g is probably ok for your molecule, but 06h is safer.
You need to use uppercase-uppercase names for the amino acid analog,
and uppercase-lowercase for the glycan. Use Os as the type for the
linking oxygen.
On Fri, Dec 14, 2012 at 12:54 PM, Urszula Uciechowska
<urszula.uciechowska.chem.umu.se> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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>
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>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Dec 14 2012 - 11:30:02 PST
