Hello,
Can you create a mol2 file with that glycam program? I think that might
import better into the Format Converter.
Wayne
On 2017-07-12 16:33, Marcos wrote:
> Hi all,
>
> I am using Analysis 2.4.2. I have been working with glycans of
> increasing complexity and I would like to facilitate my assignment in
> Analysis by using a molecular system. As you may be aware the current
> glycan built-in library in analysis is limited. My solution to this is
> going to the Glycam's website
> (http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1
> [1]) and use Carbohydrate builder to created the glycan I want.
> However, I have tried to incorporate the created glycan molecule via
> FormatConverted using various import options provided
> (coordinates:pdb, pseudo-pdb, amber (for .rst, .prmtop files? and
> CNS), chemical compound and sequence).
>
> The only option that worked for me was for a homo-olygomer: to import
> it as a chemical compound and change the atom names one by one so they
> do not repeat.
>
> Ideally I would like FormatComberter to take any PDB I create in
> glycam. Is there any solution to this?
>
> Do I have to create each chemical compound that the glycan has and
> import it with the same name as the created oligomer?
>
> If this is the case, how do I get analysis to know what type of
> linkages can be done in the new chemical compound (1,3; 1,6; etc)?
>
> MAny thanks,
>
> Marcos.
>
> Links:
> ------
> [1]
> http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1
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