That’s the idea!
> On 13 Jul 2017, at 18:31, Marcos <[log in to unmask]> wrote:
>
> Thanks!
> So basically if I have a branched pentasaccharide, I create the individual component sugars as mol2, then convert them with the script you sent and load them individually in Analysis as chemComp. Then I will be able to edit the linkages as I want within Analysis and create the full glycan, right (e.g. alpha1,2dimanose)?
> Thanks,
> Marcos.
>
>
> De: CcpNmr software mailing list <[log in to unmask]> en nombre de Wim VRANKEN <[log in to unmask]>
> Enviado: jueves, 13 de julio de 2017 04:11 p.m.
> Para: [log in to unmask]
> Asunto: Re: Analysis-Glycam web compatibility for carbohydrates and their incorporation via Format converter to Analysis
>
> Hi Marcos,
>
> At one point in CCPN’s history we teamed up with the EUROCarbDB project - the idea was to do exactly what you’re trying to do now in a consistent and large-scale manner. Unfortunately this project never got to completion, but I did write a reasonable amount of code to deal with sugars, including creating the variants for linking.
>
> In honour of the CCPN conference that’s currently taking place (hope everyone’s having fun!), and since I had a bit of time I dug up an old piece of code and modified it slightly to work by itself, Python script attached. I tried it on the also attached glucose .mol2 file from the ZINC12 website (http://zinc.docking.org/), and it seems to be working… hope it might help you (and that it works on your installation!).
> Welcome to ZINC Is Not Commercial - A database of ...
> zinc.docking.org
> Free database of over 2.7 million commercially-available compounds for virtual screening in ready-to-dock, 3D format.
>
>
> So what you do is create a .mol2 file and run the following in a terminal window:
>
> python makeFullSugar.py glucose.mol2 b-glucose
>
> Where the first argument after the script is the .mol2 file name, then the name of the sugar. To keep things simple, the script will create separate chemComps for alpha, beta and open forms - you start the name of the chemComp (the second argument) accordingly with a-, b- or o-.
>
> The script will save the chemComp and chemCompCoord files locally in the ccp/molecule/ directory - you’ll have to manually copy them to the data/cap/molecule directory of the CCPN installation.
>
> Best,
>
> Wim
>
>
>
>
> > On 13 Jul 2017, at 16:28, Marcos <[log in to unmask]> 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: miércoles, 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
>
> ---------------------------------------------------------------------------------------
> Prof. Dr. Wim Vranken
>
> [log in to unmask] Tel: +32 (0)2 6291996 (VUB)
> +32 (0)2 6505943 (IB^2)
>
> Building E, 5th Floor, E5.03, Pleinlaan 2
> 1050 Brussels, Belgium
>
> VUB - Structural Biology Brussels
>
> ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2
> Director, http://ibsquare.be/
> ---------------------------------------------------------------------------------------
>
---------------------------------------------------------------------------------------
Prof. Dr. Wim Vranken
[log in to unmask] Tel: +32 (0)2 6291996 (VUB)
+32 (0)2 6505943 (IB^2)
Building E, 5th Floor, E5.03, Pleinlaan 2
1050 Brussels, Belgium
VUB - Structural Biology Brussels
ULB-VUB - Interuniversity Institute of Bioinformatics in Brussels (IB)2
Director, http://ibsquare.be/
---------------------------------------------------------------------------------------
|
