Hi,
I also tried the glycam.org website to build a branched oligosaccharide.
There was some problem in the website I guess, because I was not able to
download the pdb or prmtop files.
On Tue, Mar 28, 2017 at 6:52 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> You may have better luck using the carbohydrate builder from
> http://glycam.org/, which was specifically designed for this purpose.
>
> -Dan
>
> On Tue, Mar 28, 2017 at 8:36 AM, Manju Sah <manjusah.gmail.com> wrote:
> > Dear Amber Users,
> >
> > I am using Amber16 and AmberTool 16 for building branched
> > oligosaccharide, using
> > Amber 14 manual as reference.
> >
> > I used following tleap commands:
> > ###################################################
> > source leaprc.protein.ff14SB
> > source leaprc.water.tip3p
> > source leaprc.GLYCAM_06j-1
> > glycan = sequence { ROH WYB 0FA }
> > set glycan tail glycan.2.O4
> > branch1 = sequence { glycan 4YB QMB 2MA 0YB }
> > set branch1 tail branch1.5.O4
> > branch2 = sequence { branch1 0YB }
> > set branch2 tail branch2.5.O6
> > branch3 = sequence { branch2 2MA WYA 0FA }
> > set branch3 tail branch3.10.O4
> > branch4 = sequence {branch3 3LA 0SA}
> > impose branch4 {3} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {3} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {4} { {H1 C1 O4 C4 60.0} }
> > impose branch4 {4} { {C1 O4 C4 H4 -60.0} }
> > impose branch4 {5} { {H1 C1 O4 C4 60.0} }
> > impose branch4 {5} { {C1 O4 C4 H4 -60.0} }
> > impose branch4 {6} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {6} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {7} { {H1 C1 O2 C2 60.0} }
> > impose branch4 {7} { {C1 O2 C2 H2 -60.0} }
> > impose branch4 {8} { {H1 C1 O4 C4 60.0} }
> > impose branch4 {8} { {C1 O4 C4 H4 -60.0} }
> > impose branch4 {9} { {H1 C1 O6 C6 -60.0} }
> > impose branch4 {9} { {C1 O6 C6 H6 60.0} }
> > impose branch4 {10} { {H1 C1 O2 C2 -60.0} }
> > impose branch4 {10} { {C1 O2 C2 H2 60.0} }
> > impose branch4 {11} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {11} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {12} { {H1 C1 O4 C4 -60.0} }
> > impose branch4 {12} { {C1 O4 C4 H4 60.0} }
> > impose branch4 {13} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {13} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {5} { {O6 C6 C5 O5 60.0} }
> > saveamberparm branch4 glycan.prmtop glycan.inpcrd
> > savepdb branch4 glycan.pdb
> > quit
> > ################################
> >
> > The oligosaccharide was minimized in vaccum and the linkages were
> > maintained.
> > Then I used the minimized structure to solvate using the following
> > commands:
> > ###############################################################
> > source leaprc.GLYCAM_06j-1
> > source leaprc.water.tip3p
> > branch4 = loadpdb glycan_min4.pdb
> > solvateBOX branch4 TIP3PBOX 10.0
> > addIons branch4 Na+ 0
> > impose branch4 {3} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {3} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {4} { {H1 C1 O4 C4 60.0} }
> > impose branch4 {4} { {C1 O4 C4 H4 -60.0} }
> > impose branch4 {5} { {H1 C1 O4 C4 60.0} }
> > impose branch4 {5} { {C1 O4 C4 H4 -60.0} }
> > impose branch4 {6} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {6} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {7} { {H1 C1 O2 C2 60.0} }
> > impose branch4 {7} { {C1 O2 C2 H2 -60.0} }
> > impose branch4 {8} { {H1 C1 O4 C4 60.0} }
> > impose branch4 {8} { {C1 O4 C4 H4 -60.0} }
> > impose branch4 {9} { {H1 C1 O6 C6 -60.0} }
> > impose branch4 {9} { {C1 O6 C6 H6 60.0} }
> > impose branch4 {10} { {H1 C1 O2 C2 -60.0} }
> > impose branch4 {10} { {C1 O2 C2 H2 60.0} }
> > impose branch4 {11} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {11} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {12} { {H1 C1 O4 C4 -60.0} }
> > impose branch4 {12} { {C1 O4 C4 H4 60.0} }
> > impose branch4 {13} { {H1 C1 O3 C3 -60.0} }
> > impose branch4 {13} { {C1 O3 C3 H3 60.0} }
> > impose branch4 {5} { {O6 C6 C5 O5 60.0} }
> > saveamberparm branch4 glycan_Solv.prmtop glycan_Solv.inpcrd
> > savepdb branch4 glycan_Solv.pdb
> > quit
> > ######################################################
> >
> > When equilibrating the solvated structure the branched linkages were
> > broken.
> >
> > The branched linkages were broken even when the prmtop was created with
> or
> > without "impose" leap command.
> >
> > Please guide me how to maintain the branched linkages in the
> > oligosaccharide.
> > Is it OK to use "bond" in leap for maintaining the linkage???🤔
> >
> >
> > Manju Kumari, PDF
> > IIT Madras, India
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thank you,
With regards,
B. Sangeetha
Ph.D Scholar,
Centre for Bioinformatics,
Pondicherry University,
Pondicherry,
India
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Received on Wed Mar 29 2017 - 02:30:03 PDT
