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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Received on Wed Mar 29 2017 - 03:00:02 PDT
