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
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--
-------------------------
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
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Received on Tue Mar 28 2017 - 06:30:04 PDT
