Since you have generated your own charges for the molecule, you should
not need to change the residue name. The residue name provides leap
with charge and structural information if a corresponding residue
template (prep or lib) is loaded.
I presume that this will be inserted into a chain of some sort so that
filling in the open valences is not necessary. If you do need leap to
fill in atoms, then you would need to provide leap with a template for
doing so, but the template can use the same residue name if you build
it yourself.
On Fri, Dec 14, 2012 at 3:18 PM, Urszula Uciechowska
<urszula.uciechowska.chem.umu.se> wrote:
> Thank you , its working now.
> I have one more question in my case, should I set restype for sugar/protein or I can skip that?
> /Urszula
>
> --------------------------------
> Urszula Uciechowska, Ph.D.
> Department of Chemistry
> Umeå University
> SE-901 87 Umeå, Sweden
> urszula.uciechowska.chem.umu.se
> ________________________________________
> Von: Lachele Foley (Lists) [lf.list.gmail.com]
> Gesendet: Freitag, 14. Dezember 2012 20:09
> An: AMBER Mailing List
> Betreff: Re: [AMBER] glycam_06h atom types
>
> 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
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> 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
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Dec 14 2012 - 13:30:01 PST
