Hi,
I couple of comments. I think what Oliver said is incorrect - a
beta-cyclodextrin is composed of alpha-1,4-glucose residues. Thus, each
residue is name 4GA by Glycam residue naming convention (see the Amber
manual). 4YB would be for beta-1-4 linked GlcNAc.
Using Amber's xleap, you can load Glycam06's residues and view what each
atom is named. With that knowledge, you can then manually modify the
cyclodextrin's crystal PDB file appropriately. If you are new to Amber, you
should do some tutorial first and read the manual, especially the chapters
on force fields and Leap (aka tleap and xleap). If you are modeling a
protein and carbohydrate system, then load all of the necessary force-field
files and input structures into leap to create a single topology file. If
you new to carbohydrate chemistry, then you need to learn about this field
also. For example, the atom naming across different carbohydrates is fairly
uniform (e.g. each pyranose ring atom is name C1, C2, C3, ...etc.).
Best regards,
Karl
On Mon, Feb 17, 2020 at 5:20 PM Oliver Grant <olivercgrant.gmail.com> wrote:
> Hi Marcelo,
>
> I don't understand what your GAG question is. Can you clarify?
> In general you can find "Glycam nomenclature" or "Glycam naming" here:
> http://glycam.org/docs/forcefield/glycam-naming-2/ (or by searching for
> those terms). For cyclodextrin each residue should be named 4YB. I'm
> guessing that they have entered it into the PDB as one big residue that
> you'll have to manually break up into GlcNAc residues. You can find out
> what the atom names should be by inspecting the prep files here:
> $AMBERHOME//dat/leap/prep/GLYCAM_06j-1.prep. Note that the GLYCAM version
> and thus prep file name you have may be different depending on what version
> of Amber you have installed. If you search for 4YB you'll find the entry
> and then see the atom names listed.
>
> Best,
>
> Oliver
>
>
> On Sun, Feb 16, 2020 at 6:50 PM Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com> wrote:
>
> > Dear Lachele Foley, thanks for the reply.
> >
> > I am now starting collaborations with the study of sugars and their
> > monosaccharide derivatives.
> >
> > I used GLYCAM-web to obtain parameters for glycosaminoglycans and another
> > work started (which I have some doubts, but I write later).
> >
> > My lack of experience here is how and where to get the types of atoms and
> > names of residues to edit the columns of the PDB file that will be
> loaded,
> > after using the Glycam force field in xleap ...?
> >
> > I think I will have to use a three-letter residue identification for each
> > monomer, and I don't know where to get it from.
> >
> > I will have to edit the column of type of atoms suitable for Glycam, and
> I
> > also don't know how to obtain it.
> >
> > So, my doubts to follow are in what types of atoms to use and their
> residue
> > names to repeat in all the structures of the monosaccharide monomer that
> > forms the circular structure of the cyclodextrins.
> >
> > Below I highlight part of the beta-cyclodextrin file and part of the
> > glycosaminoglycan file, to indicate the locations of my doubts for
> editing
> > the PDB file.
> >
> > Thank you if you can show me the way forward.
> >
> > graciously
> >
> >
> > beta-cyclodextrin file
> >
> >
> ________________________________________________________________________________
> > *A B*
> >
> > HETATM10131 *C11 BCD* A 601 39.077 58.096 52.284 1.00 49.61
> > C
> > HETATM10132 *C21 BCD* A 601 37.790 58.453 51.518 1.00 48.70
> > C
> > HETATM10133 *O21 BCD* A 601 37.531 59.846 51.581 1.00 50.53
> > O
> > HETATM10134 C31 BCD A 601 36.593 57.694 52.087 1.00 48.23
> > C
> > HETATM10135 O31 BCD A 601 35.450 57.947 51.275 1.00 53.18
> > O
> > HETATM10136 C41 BCD A 601 36.852 56.179 52.159 1.00 46.59
> > C
> > HETATM10137 O41 BCD A 601 35.823 55.581 52.994 1.00 46.12
> > O
> > HETATM10138 C51 BCD A 601 38.247 55.871 52.772 1.00 47.11
> > C
> > HETATM10139 O51 BCD A 601 39.291 56.696 52.195 1.00 48.63
> > O
> > HETATM10140 C61 BCD A 601 38.665 54.432 52.515 1.00 47.75
> > C
> > HETATM10141 O61 BCD A 601 39.321 54.276 51.242 1.00 48.15
> > O
> > HETATM10142 C12 BCD A 601 35.369 54.415 52.377 1.00 49.11
> > C
> > HETATM10143 C22 BCD A 601 33.907 54.759 52.706 1.00 51.56
> > C
> > HETATM10144 O22 BCD A 601 33.652 56.126 52.419 1.00 53.88
> > O
> > HETATM10145 C32 BCD A 601 33.597 54.489 54.182 1.00 50.46
> > C
> > HETATM10146 O32 BCD A 601 32.201 54.682 54.413 1.00 51.18
> > O
> > HETATM10147 C42 BCD A 601 34.018 53.060 54.596 1.00 49.07
> > C
> >
> >
> _____________________________________________________________________________
> >
> > glycosaminoglycan file
> >
> >
> _____________________________________________________________________________
> > LINK O OME 1 C1 WYS 2
> > LINK O4 WYS 2 C1 YZB 3
> > LINK O3 WYS 2 S1 SO3 11
> > LINK O4 YZB 3 C1 3YS 4
> > LINK O2 YZB 3 S1 SO3 10
> > LINK O3 3YS 4 C1 YZB 5
> > LINK O4 YZB 5 C1 UVB 6
> > LINK O2 YZB 5 S1 SO3 9
> > LINK O6 UVB 6 S1 SO3 7
> > LINK O4 UVB 6 S1 SO3 8
> > HETATM 1 *H1 OME * 1 3.753 7.497 -1.193 1.00 0.00
> > H
> > HETATM 2 *CH3 OME* 1 2.889 7.153 -1.762 1.00 0.00
> > C
> > HETATM 3 *H2 OME* 1 2.661 7.876 -2.545 1.00 0.00
> > H
> > HETATM 4 * H3 OME * 1 2.034 7.076 -1.090 1.00 0.00
> > H
> > HETATM 5 *O OME* 1 3.162 5.841 -2.353 1.00 0.00
> > O
> > HETATM 6 *C1 WYS* 2 4.341 5.786 -3.245 1.00 0.00
> > C
> > HETATM 7 *H1 WYS * 2 4.274 6.618 -3.947 1.00 0.00
> > H
> > HETATM 8 *C2 WYS * 2 4.360 4.474 -4.077 1.00 0.00
> > C
> > HETATM 9 *H2 WYS* 2 4.986 4.667 -4.948 1.00 0.00
> > H
> > HETATM 10 N2 WYS 2 2.987 4.193 -4.533 1.00 0.00
> > N
> > HETATM 11 H2N WYS 2 2.250 4.499 -3.916 1.00 0.00
> > H
> > HETATM 12 S1 WYS 2 2.584 3.453 -5.993 1.00 0.00
> > S
> > HETATM 13 O1S WYS 2 3.261 4.177 -7.037 1.00 0.00
> > O
> > HETATM 14 O2S WYS 2 1.154 3.571 -6.095 1.00 0.00
> > O
> > HETATM 15 O3S WYS 2 2.999 2.077 -5.903 1.00 0.00
> > O
> > HETATM 16 C3 WYS 2 4.920 3.255 -3.304 1.00 0.00
> > C
> > HETATM 17 H3 WYS 2 4.105 2.863 -2.692 1.00 0.00
> > H
> > HETATM 18 C4 WYS 2 6.082 3.557 -2.337 1.00 0.00
> > C
> > HETATM 19 H4 WYS 2 7.006 3.680 -2.896 1.00 0.00
> > H
> > HETATM 20 C5 WYS 2 5.874 4.833 -1.515 1.00 0.00
> > C
> > HETATM 21 H5 WYS 2 5.000 4.699 -0.875 1.00 0.00
> > H
> > HETATM 22 C6 WYS 2 7.041 5.251 -0.607 1.00 0.00
> > C
> > HETATM 23 H62 WYS 2 7.223 4.486 0.148 1.00 0.00
> > H
> > HETATM 24 H61 WYS 2 6.799 6.182 -0.092 1.00 0.00
> > H
> > HETATM 25 O6 WYS 2 8.235 5.442 -1.381 1.00 0.00
> > O
> > HETATM 26 H6O WYS 2 8.964 5.662 -0.797 1.00 0.00
> > H
> > HETATM 27 O5 WYS 2 5.593 5.927 -2.469 1.00 0.00
> > O
> > HETATM 28 O4 WYS 2 6.181 2.407 -1.419 1.00 0.00
> > O
> > HETATM 29 O3 WYS 2 5.338 2.171 -4.231 1.00 0.00
> > O
> > HETATM 30 C1 YZB 3 7.519 1.825 -1.246 1.00 0.00
> > C
> > HETATM 31 H1 YZB 3 8.186 2.585 -0.844 1.00 0.00
> > H
> > HETATM 32 O5 YZB 3 8.061 1.359 -2.539 1.00 0.00
> > O
> > HETATM 33 C5 YZB 3 9.341 0.645 -2.445 1.00 0.00
> > C
> > _______________________________________________________________________
> > Dr. Marcelo Andrade Chagas,
> > http://lattes.cnpq.br/7024808363863350
> > *eCsMo**Lab**: Laboratório de Estudos Computacionais em Sistemas
> > Moleculares*
> > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> > * http://lqcmm.qui.ufmg.br/
> >
> > Departamento de Química, ICEx, Universidade Federal de Minas Gerais
> >
> > 31270-901, Pampulha, Belo Horizonte, MG, Brazil.
> > Tel:(31)3409-5776
> >
> >
> > Lachele Foley <lf.list.gmail.com> escreveu no dia sexta, 14/02/2020 à(s)
> > 21:25:
> >
> > > The site can't do that yet.
> > >
> > > The simplest thing to do would be to find a structure for the molecule
> > > somewhere, then change the names of the residues - and atoms as needed
> > > - so that they can be processed by leap using the glycam force field.
> > >
> > > Here is a structure containing beta-cyclodextrin:
> > > https://www.rcsb.org/structure/1g1y
> > >
> > > Let me know if you need help proceeding from there.
> > >
> > > On Fri, Feb 14, 2020 at 3:41 PM Marcelo Andrade Chagas
> > > <andrade.mchagas.gmail.com> wrote:
> > > >
> > > > Dear AMBER developers
> > > >
> > > > How to get topology for alfa-cyclodextrin, beta-cyclodextrin and
> > > > gama-cyclodextrin.
> > > >
> > > > I tried Glicam-web for β-cyclodextrin <
> https://www.rcsb.org/ligand/BCD
> > >.
> > > But
> > > > he reported the following message:
> > > >
> > > > *GLYCAM-Web has detected that you wish to build a system containing a
> > > > cycle. We are sorry, but at this time we cannot process such
> requests.
> > If
> > > > you would like, contact us about this.*
> > > >
> > > > Best regards,
> > > >
> > > > Dr. Marcelo Andrade Chagas,
> > > > http://lattes.cnpq.br/7024808363863350
> > > > *eCsMo**Lab**: Laboratório de Estudos Computacionais em Sistemas
> > > > Moleculares*
> > > > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> > > > * http://lqcmm.qui.ufmg.br/
> > > >
> > > > Departamento de Química, ICEx, Universidade Federal de Minas Gerais
> > > >
> > > > 31270-901, Pampulha, Belo Horizonte, MG, Brazil.
> > > > Tel:(31)3409-5776
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> > >
> > > _______________________________________________
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> > >
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Received on Mon Feb 17 2020 - 12:00:02 PST
