Hello,
Do you need the coordinates or just the topology? I was assuming the
latter. This would be the Import -> Single files -> Chemical compounds
option.
Wayne
On 2017-07-13 15:28, Marcos wrote:
> Hi,
>
> I converted *.pdb to *mol2 and it did not work either. Wen I do
> Impor->Single File ->Coordinates
>
> I then selected different options (pdb pseudo-pdb, CNS, amber) and the
> most informative (to me) error I got was None chemComp 3 letter
> code... Do you want to select a chemComp for this residue?
>
> This error is what prompted me to ask in my previous email about
> loading single sugar residues and naming them with the same 3-letter
> code used in the full glycan (they use Glycam naming convention).
>
> Any ideas?
>
> Thanks,
>
> Marcos.
>
> -------------------------
>
> DE: CcpNmr software mailing list <[log in to unmask]> en nombre de
> W. Boucher <[log in to unmask]>
> ENVIADO: miƩrcoles, 12 de julio de 2017 08:34 p.m.
> PARA: [log in to unmask]
> ASUNTO: Re: Analysis-Glycam web compatibility for carbohydrates and
> their incorporation via Format converter to Analysis
>
> 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
> [1]
>
>
> Links:
> ------
> [1]
> http://glycam.org/tools/molecular-dynamics/oligosaccharide-builder/build-glycan?id=1
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