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Merge pull request #1134 from haddocking/BDP-glycan
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add new glycans
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@mgiulini
mgiulini authored Nov 20, 2024
2 parents 8263b9b + 7bc9f2d commit 84b5a1e
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9 changes: 9 additions & 0 deletions src/haddock/cns/toppar/carbohydrate.param
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Expand Up @@ -57,6 +57,7 @@ BOND CCA NH1 1000.0 1.45 !as extended atom carbon-N
BOND CCS C 1000.0 1.52 !" " " " -C
BOND CCE C 1000.0 1.52
BOND CCA C 1000.0 1.52
BOND CC6 OC 1000.0 1.25 ! standard CO bond (parm10)


ANGLe H OH1 CCS 500.0 109.35
Expand Down Expand Up @@ -148,6 +149,10 @@ ANGLe C CCE OES 500.0 107.24
ANGLe C CCA OES 500.0 107.24
ANGLe C CCE CCS 500.0 108.72
ANGLe C CCA CCS 500.0 108.72
! other angles
ANGLe OC CC6 OC 500.00 123.3548
ANGLe CCS CC6 OC 500.0 109.70 ! guess from CCS-CC6-OAS (to check: experimental structures have 112-113)



DIHEdral X CCS CCS X 2.0 3 0.0
Expand All @@ -174,6 +179,7 @@ DIHEdral X C CCA X 2.0 3 0.0
DIHEdral X C CCS X 2.0 3 0.0 ! N-acetyl in NAG, 8/30/93
DIHEdral CCS NH1 C CCS 2.0 2 0.0 ! peptide plane in NAG
! guess - PDA 8/99
DIHEdral CCS OES CCE CCS 2.0 2 0.0 ! guessing for BDP

IMPRoper CCS X X CCS 500.0 0 35.26439
IMPRoper CCE X X CCS 500.0 0 35.26439
Expand Down Expand Up @@ -205,6 +211,7 @@ IMPRoper HAS CCE OAS CCS 500.00 0 66.8
IMPRoper HAS HAS CCE CCS 500.00 0 70.3 !SIA C3
IMPRoper HAS HAS CCS CCE 500.00 0 70.3 !SIA C3
IMPRoper HAS HAS CCA CCS 500.00 0 70.3
IMPRoper HAS HAS CCS CCS 500.00 0 70.3 !ABE C3
IMPRoper HAS OH1 CCS CCS 500.00 0 66.9 !MAN,GLC,GLA,NAG,FCA,XYP C3 - A2G,FCA,SIA C4 - SIA C7,C8
IMPRoper HAS OAS CCS CCS 500.00 0 66.9
IMPRoper HAS CCS OH1 CCS 500.00 0 66.8 !FUC C3 MAN,GLC,GLA,NAG,FUC,XYP C4
Expand All @@ -231,6 +238,8 @@ IMPRoper HAS OES OAS CCS 500.00 0 67.6 !A12,A13,A14,A16,B12L,B14L alph
IMPRoper C CCS NH1 O 500.00 0 0.0 !NAG,SIA planar
IMPRoper NH1 C CCS H 500.00 0 0.0 !NAG,SIA planar
IMPRoper CCS NH1 C CCS 500.00 0 180.0 !NAG,SIA trans peptide
! new impropers
IMPRoper CC6 CCS OC OC 500.00 0 0.0 !BDP, angle taken from charmm


{Asn-NAG}
Expand Down
305 changes: 303 additions & 2 deletions src/haddock/cns/toppar/carbohydrate.top
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Expand Up @@ -6,6 +6,8 @@ REMARKS Topologies updated to Feng, PLoS One, 2017
REMARKS PMC 5726640
REMARKS Alexandre Bonvin July-2020
REMARKS Patches added for GAL-SIA 2-3 and 2.6 linkages
REMARKS Marco Giulini November-2024
REMARKS Topologies added for BDP-MMA-XYS-ABE
REMARKS ----------------------------------------------------------
REMARKS Currently supported carbohydrates and their anomers:
REMARK (codes in parenthesis are commonly used alternatives - currently not recognized by CNS):
Expand All @@ -26,6 +28,10 @@ REMARKS FCB: beta -D-fucopyranose
REMARKS SIA: alpha-N-acetyl neuraminic acid
REMARKS SIB: beta-N-acetyl neuraminic acid - A. Bonvin
REMARKS XYP: beta-D-xylopyranose
REMARKS BDP: beta-D-glucoronic acid
REMARKS MMA: methyl alpha-D-mannopyranoside
REMARKS XYS: alpha-D-xylopyranose
REMARKS ABE: alpha-D-Abequopyranose
REMARKS ----------------------------------------------------------
REMARKS Links
REMARKS B1N: N-linked glycan beta link from NAG and NDG to ASN (asparagine)
Expand Down Expand Up @@ -1921,6 +1927,303 @@ RESIdue GXL !alpha-L-galactopyranose

END

RESIdue BDP !beta-D-glucoronic acid
GROUP

ATOM C1 TYPE=CCE CHARge= 0.340 END
ATOM H1 TYPE=HAS CHARge= 0.090 END
ATOM O1 TYPE=OH1 CHARge=-0.650 END
ATOM HO1 TYPE=H CHARge= 0.420 END
ATOM C5 TYPE=CCS CHARge= 0.110 END
ATOM H5 TYPE=HAS CHARge= 0.090 END
ATOM O5 TYPE=OES CHARge=-0.400 END
ATOM C2 TYPE=CCS CHARge= 0.140 END
ATOM H2 TYPE=HAS CHARge= 0.090 END
ATOM O2 TYPE=OH1 CHARge=-0.650 END
ATOM HO2 TYPE=H CHARge= 0.420 END
ATOM C3 TYPE=CCS CHARge= 0.140 END
ATOM H3 TYPE=HAS CHARge= 0.090 END
ATOM O3 TYPE=OH1 CHARge=-0.650 END
ATOM HO3 TYPE=H CHARge= 0.420 END
ATOM C4 TYPE=CCS CHARge= 0.140 END
ATOM H4 TYPE=HAS CHARge= 0.090 END
ATOM O4 TYPE=OH1 CHARge=-0.650 END
ATOM HO4 TYPE=H CHARge= 0.420 END
ATOM C6 TYPE=CC6 CHARge= 0.520 END
ATOM O61 TYPE=OC CHARge=-0.760 END
ATOM O62 TYPE=OC CHARge=-0.760 END

BOND C1 O1
BOND C1 H1
BOND O1 HO1
BOND C1 O5
BOND C1 C2
BOND C2 H2
BOND C2 O2
BOND O2 HO2
BOND C2 C3
BOND C3 H3
BOND C3 O3
BOND O3 HO3
BOND C3 C4
BOND C4 H4
BOND C4 O4
BOND O4 HO4
BOND C4 C5
BOND C5 H5
BOND C5 C6
BOND C6 O61
BOND C6 O62
BOND C5 O5

DIHEDRAL O5 C1 C2 C3
DIHEDRAL C1 C2 C3 C4
DIHEDRAL C2 C3 C4 C5
DIHEDRAL C3 C4 C5 O5
DIHEDRAL C4 C5 O5 C1
DIHEDRAL C4 C5 C6 O61
DIHEDRAL O5 C1 O1 HO1
DIHEDRAL C1 C2 O2 HO2
DIHEDRAL C2 C3 O3 HO3
DIHEDRAL C3 C4 O4 HO4
DIHEDRAL C5 O5 C1 C2 ! the only one not defined in haddock

IMPRoper C6 C5 O62 O61

IMPRoper H1 O1 O5 C2 {beta C1}
IMPRoper H2 C1 O2 C3 {C2}
IMPRoper H3 O3 C2 C4 {C3}
IMPRoper H4 C3 O4 C5 {C4}
IMPRoper H5 C4 O5 C6 {C5}
IMPRoper H61 H62 O6 C5 !stereo C6
END

RESIdue MMA ! methyl alpha-D-mannopyranoside ! axial O-methyl group added to C1 on mannose
GROUP
ATOM C1 TYPE=CCE CHARge= 0.290 END ! lowered partial charge according to charmm36
ATOM H1 TYPE=HAS CHARge= 0.100 END
ATOM O1 TYPE=OAS CHARge=-0.360 END ! lowered partial charge according to charmm36 and changed atom type as in MAG
! ATOM HO1 TYPE=H CHARge= 0.400 END ! deleted HO1
ATOM C7 TYPE=CCS CHARge=-0.090 END ! C7 defined as CCS for consistency with MAG.
ATOM H71 TYPE=HAS CHARge= 0.090 END ! methyl hydrogens with charmm charges
ATOM H72 TYPE=HAS CHARge= 0.090 END
ATOM H73 TYPE=HAS CHARge= 0.090 END
ATOM C2 TYPE=CCS CHARge= 0.150 END
ATOM O2 TYPE=OH1 CHARge=-0.650 END
ATOM H2 TYPE=HAS CHARge= 0.100 END
ATOM HO2 TYPE=H CHARge= 0.400 END
ATOM C3 TYPE=CCS CHARge= 0.150 END
ATOM H3 TYPE=HAS CHARge= 0.100 END
ATOM O3 TYPE=OH1 CHARge=-0.650 END
ATOM HO3 TYPE=H CHARge= 0.400 END
ATOM C4 TYPE=CCS CHARge= 0.150 END
ATOM H4 TYPE=HAS CHARge= 0.100 END
ATOM O4 TYPE=OH1 CHARge=-0.650 END
ATOM HO4 TYPE=H CHARge= 0.400 END
ATOM C5 TYPE=CCS CHARge= 0.100 END
ATOM H5 TYPE=HAS CHARge= 0.100 END
ATOM O5 TYPE=OES CHARge=-0.400 END
ATOM C6 TYPE=CC6 CHARge= 0.050 END
ATOM H61 TYPE=HAS CHARge= 0.100 END
ATOM H62 TYPE=HAS CHARge= 0.100 END
ATOM O6 TYPE=OH1 CHARge=-0.650 END
ATOM HO6 TYPE=H CHARge= 0.400 END

BOND C1 O1
BOND C1 H1
BOND C1 O5
BOND C1 C2
BOND C2 H2
BOND C2 O2
BOND O2 HO2
BOND C2 C3
BOND C3 H3
BOND C3 O3
BOND O3 HO3
BOND C3 C4
BOND C4 H4
BOND C4 O4
BOND O4 HO4
BOND C4 C5
BOND C5 H5
BOND C5 C6
BOND C6 H61
BOND C6 H62
BOND C6 O6
BOND O6 HO6
BOND C5 O5
BOND O1 C7
BOND C7 H71
BOND C7 H72
BOND C7 H73

DIHEDRAL C1 C2 C3 C4
DIHEDRAL C2 C3 C4 C5
DIHEDRAL C3 C4 C5 O5
DIHEDRAL C4 C5 O5 C1
DIHEDRAL C5 O5 C1 C2
DIHEDRAL O5 C1 C2 C3
DIHEDRAL H2 C2 O2 HO2
DIHEDRAL H3 C3 O3 HO3
DIHEDRAL H4 C4 O4 HO4
DIHEDRAL H5 C5 C6 O6
DIHEDRAL C5 C6 O6 H61
DIHEDRAL O5 C1 O1 C7 ! the first not in HADDOCK: C7 dihedral
! DIHEDRAL C1 O1 C7 H71 ! the second not in HADDOCK. commented out in agreement with MAG

! IMPRoper C1 H1 O5 C2 ! alpha-anomer
! IMPRoper C1 O5 O1 C2 ! alpha-anomer definition using non-hydrogen atoms, ATB 12/06/09

! IMPRoper C2 O2 C1 C3 {axial C2}
! IMPRoper C3 O3 C2 C4
! IMPRoper C4 C3 O4 C5
! IMPRoper C5 C6 C4 O5

IMPRoper H1 O5 O1 C2 {alpha C1}
IMPRoper H2 O2 C1 C3 {C2}
IMPRoper H3 O3 C2 C4 {C3}
IMPRoper H4 C3 O4 C5 {C4}
IMPRoper H5 C4 O5 C6 {C5}
IMPRoper H61 H62 O6 C5 !stereo C6


END

RESIdue XYS !alpha-D-xylopyranose
GROUP
ATOM C1 TYPE=CCE CHARge= 0.350 END
ATOM H1 TYPE=HAS CHARge= 0.100 END
ATOM O1 TYPE=OH1 CHARge=-0.650 END
ATOM HO1 TYPE=H CHARge= 0.400 END
ATOM C2 TYPE=CCS CHARge= 0.150 END
ATOM O2 TYPE=OH1 CHARge=-0.650 END
ATOM H2 TYPE=HAS CHARge= 0.100 END
ATOM HO2 TYPE=H CHARge= 0.400 END
ATOM C3 TYPE=CCS CHARge= 0.150 END
ATOM H3 TYPE=HAS CHARge= 0.100 END
ATOM O3 TYPE=OH1 CHARge=-0.650 END
ATOM HO3 TYPE=H CHARge= 0.400 END
ATOM C4 TYPE=CCS CHARge= 0.150 END
ATOM H4 TYPE=HAS CHARge= 0.100 END
ATOM O4 TYPE=OH1 CHARge=-0.650 END
ATOM HO4 TYPE=H CHARge= 0.400 END
ATOM C5 TYPE=CCS CHARge= 0.100 END
ATOM O5 TYPE=OES CHARge=-0.400 END
ATOM H51 TYPE=HAS CHARge= 0.100 END
ATOM H52 TYPE=HAS CHARge= 0.100 END

BOND C1 O1
BOND C1 H1
BOND O1 HO1
BOND C1 O5
BOND C1 C2
BOND C2 H2
BOND C2 O2
BOND O2 HO2
BOND C2 C3
BOND C3 H3
BOND C3 O3
BOND O3 HO3
BOND C3 C4
BOND C4 H4
BOND C4 O4
BOND O4 HO4
BOND C4 C5
BOND C5 H51
BOND C5 H52
BOND C5 O5

DIHEDRAL C1 C2 C3 C4
DIHEDRAL C2 C3 C4 C5
DIHEDRAL C3 C4 C5 O5
DIHEDRAL C4 C5 O5 C1
DIHEDRAL C5 O5 C1 C2
DIHEDRAL O5 C1 C2 C3
DIHEDRAL H1 C1 O1 HO1
DIHEDRAL H2 C2 O2 HO2
DIHEDRAL H3 C3 O3 HO3
DIHEDRAL H4 C4 O4 HO4

IMPRoper H1 O5 O1 C2 {alpha C1}
IMPRoper H2 C1 O2 C3 {C2}
IMPRoper H3 O3 C2 C4 {C3}
IMPRoper H4 C3 O4 C5 {C4}
IMPRoper H51 H52 O5 C4 {C5}

END

RESIdue ABE !alpha-D-Abequopyranose
GROUP

ATOM C1 TYPE=CCE CHARge= 0.340 END
ATOM H1 TYPE=HAS CHARge= 0.090 END
ATOM O1 TYPE=OH1 CHARge=-0.650 END
ATOM HO1 TYPE=H CHARge= 0.420 END
ATOM C5 TYPE=CCS CHARge= 0.110 END
ATOM H5 TYPE=HAS CHARge= 0.090 END
ATOM O5 TYPE=OES CHARge=-0.400 END
ATOM C2 TYPE=CCS CHARge= 0.140 END
ATOM H2 TYPE=HAS CHARge= 0.090 END
ATOM O2 TYPE=OH1 CHARge=-0.650 END
ATOM HO2 TYPE=H CHARge= 0.420 END
ATOM C3 TYPE=CCS CHARge=-0.180 END
ATOM H31 TYPE=HAS CHARge= 0.090 END
ATOM H32 TYPE=HAS CHARge= 0.090 END
ATOM C4 TYPE=CCS CHARge= 0.140 END
ATOM H4 TYPE=HAS CHARge= 0.090 END
ATOM O4 TYPE=OH1 CHARge=-0.650 END
ATOM HO4 TYPE=H CHARge= 0.420 END
ATOM C6 TYPE=CC6 CHARge=-0.270 END
ATOM H61 TYPE=HAS CHARge= 0.090 END
ATOM H62 TYPE=HAS CHARge= 0.090 END
ATOM H63 TYPE=HAS CHARge= 0.090 END

BOND C1 O1
BOND C1 H1
BOND O1 HO1
BOND C1 O5
BOND C1 C2
BOND C2 H2
BOND C2 O2
BOND O2 HO2
BOND C2 C3
BOND C3 H31
BOND C3 H32
BOND C3 C4
BOND C4 H4
BOND C4 O4
BOND O4 HO4
BOND C4 C5
BOND C5 H5
BOND C5 C6
BOND C6 H61
BOND C6 H62
BOND C6 H63
BOND C5 O5

! dihedrals taken from alpha mannose
DIHEDRAL C1 C2 C3 C4
DIHEDRAL C2 C3 C4 C5
DIHEDRAL C3 C4 C5 O5
DIHEDRAL C4 C5 O5 C1
DIHEDRAL C5 O5 C1 C2
DIHEDRAL O5 C1 C2 C3
DIHEDRAL H1 C1 O1 HO1
DIHEDRAL H2 C2 O2 HO2
! DIHEDRAL H3 C3 O3 HO3 ! not present anymore, substituted by the H31 H32 C4 C2 improper taken from SIA
DIHEDRAL H4 C4 O4 HO4
! DIHEDRAL H5 C5 C6 O6 ! not present anymore (missing O6)
! DIHEDRAL C5 C6 O6 H61 ! not present anymore (missing O6)
DIHEDRAL H5 C5 C6 H61 ! taken from fucoses and RAM

IMPRoper H31 H32 C4 C2 {C3} ! this improper is used in SIA but there the atom type of C2 is not CCS but CCE.
IMPRoper H1 O5 O1 C2 {alpha C1}
IMPRoper H2 C1 O2 C3 {C2}
IMPRoper H4 O4 C3 C5 {C4}
IMPRoper H5 C4 O5 C6 {C5}

END

!-------------------------------------------------------------------
!-------------------------------------------------------------------

Expand Down Expand Up @@ -2790,5 +3093,3 @@ END
!-------------------------------------------------------------------

set message=$old_message echo=$old_echo end


5 changes: 3 additions & 2 deletions src/haddock/modules/topology/topoaa/cns/bondglycans.cns
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Original file line number Diff line number Diff line change
Expand Up @@ -22,11 +22,12 @@ display
define
(
{- define all alpha anomer carbo residues for the links below -}
alpha= ( resname GLC or resname GLA or resname MAN or resname NDG or resname A2G or resname FUC or resname FCA or resname NDG);
alpha= ( resname GLC or resname GLA or resname MAN or resname NDG or resname A2G or resname FUC or resname FCA or resname NDG
or resname MMA or resname XYS or resname RAM or resname ABE);

{- define all beta anomer carbo residues for the links below -}
beta= ( resname BGC or resname GAL or resname BMA or resname NAG or resname NGA or resname FUL or resname FCB or resname XYP
or resname NAG or resname NGA);
or resname NAG or resname NGA or resname BDP);

{- Maximum distance between linkable atoms -}
carbo_dist= 2.0;
Expand Down

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