Couldn't test yet, but I will.
Doing it by hand will work. Do you need more help with that?
On Tue, Feb 18, 2020 at 11:20 AM Lachele Foley <lf.list.gmail.com> wrote:
>
> Yes... 4GA's all around for BCD. The annoying part is that all the
> residues are in one residue to start with, so changing the names is
> really tedious.
>
> We have a nascent program to automatically rename the residues and
> atoms. I plan to test it on this system, probably tonight. I'll
> report here.
>
> On Mon, Feb 17, 2020 at 2:34 PM Karl Kirschner <k.n.kirschner.gmail.com> wrote:
> >
> > 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
> > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 19 2020 - 19:30:01 PST
