The best detail that exists can be found in: (a) the top of the .dat
param file, and (b) by chemical analogy to existing entries in the
.prep file. Since guluronic acid would differ from, say, galacturonic
acid, only by stereochemisty, it should be simple enough to determine
the atom types by analogy to the prep entry for galacturonic acid (0OB
or 0OA). If you have a reducing-terminal OH, see entry ROH. If it is
an -OMe, use OME, etc.
On Thu, Feb 19, 2015 at 6:42 AM, Gustavo Seabra
<gustavo.seabra.gmail.com> wrote:
> Hi Lachele,
>
> Thank you very much for your answer.
>
> Yes, I’m aware of the uppercase-lowercase atom types, and those are the ones I’m trying to use. I have identified most of the atom types. However, some types are still not clear to me. (Do you know of any source that describes the available atom types in detail?)
>
> As for the GLYCAM-web files, I just noticed that I was looking at atom names instead of types. I just located the atom types in the generated prmtop file. Sorry!
>
> Thank you very much,
> Gustavo Seabra
>
>
>
>> Em 19/02/2015, à(s) 00:16, Lachele Foley <lf.list.gmail.com> escreveu:
>>
>> You need to use the uppercase-lowercase atom types in the current parm
>> files, and use the current parm files. Set the types in your unit by
>> the chemical type defined in the parm file. It might be simplest to
>> try to match those in a similar prep file. For example, you might see
>> the prep entry for 0OB (zero capital-O capital=B), for galacturonic
>> acid.
>>
>> I don't know what you mean by a unit created by GLYCAM-Web that uses
>> all uppercase atom type names. From which URL did you generate or
>> download this unit?
>>
>>
>>
>> On Wed, Feb 18, 2015 at 1:54 PM, Gustavo Seabra
>> <gustavo.seabra.gmail.com> wrote:
>>> Dear all,
>>>
>>> We are trying to create a custom monosaccharide unit using GLYCAM force field, but we are having a bit of trouble choosing the atom types to use.
>>>
>>> To understand more about the atom types to use, we have tried creating a related unit in Glycam-web, but the unit created seems to use different atom types than the ones available in the force field. Specifically, in the GLYCAM_06j.dat file, all atoms have uppercase first letters and lowercase second letters, while the unit created by GLYCAM-Web has all uppercase letters.
>>>
>>> Could anyone help us identifying the correct atom types in Glycam force field to use? (BTW, the unit we're trying to build is guluronic acid, as preset in alginate.)
>>>
>>> Thank you,
>>> Gustavo Seabra
>>>
>>>
>>>
>>>
>>> _______________________________________________
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>>> 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 Feb 20 2015 - 11:00:03 PST
