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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Feb 18 2015 - 19:30:02 PST
