ssnmr (c41b1)
Solid State NMR (SSNMR) Energy Functions
This module makes the SSNMR energy functions satisfying experimental data
observed in solid-state NMR. It focuses on 15N-chemical shifts and 15N-1H
dipolar couplings in a solid state. A set of these energy potentials are called
as orientational restraints providing us with the orientation information, such
as tilt, rotation, and etc. of in a particular helix. The module is specialized
on determining helix orientations in a bilayer.
Please report problems to mack97hyuk@gmail.com or wonpil@ku.edu
References : J. Lee, J. Chen, C. L. Brooks III, and W. Im,
J. Magn. Reson. 193, 68-76(2008)
: it includes the explanation of developement and application for
these restraints.
* 15N Chemical shift : Syntax :: Syntax of 15N chemical shift
* 15N Cheimical shift : Charmm input :: Example of 15N chemical shift
* 15N-1H dipolar coupling: Syntax :: Syntax of 15N-1H dipolar coupling
* 15N-1H dipolar coupling: Charmm input :: Example of 15N-1H dipolar coupling
File: SSNMR, Node: 15N Chemical shift : Syntax, Up: Top, Next: 15N Chemical shift : Charmm input, Previous: Top
1. 15N chemical shift
[SYNTAX]
CCS
EXPS [S11 real] [S22 real] [S33 real] [PHI real]
ASSIGN atom-selection [FORCe real] [EXP real]
RESEt
PRINt ANALysis
END
S11, S22, S33: Chemical shift tensors (ppm). They are obtained by diagonalizing
a shielding tensor. These values are given from experiments.
Refer Table1 in the above reference.
PHI: Phi angle (degrees) is defined by a rotation angle between NH
vector and S11 chemical tensor on the peptide plane. It depends
on the residues and also experimental conditions.
FORCe: Force constant (unit: kcal/mol/ppm^2).
EXP: Chemical shift observables from experiment (ppm).
atom-selection: Three atoms (NH, C, and O in peptide plane) consisting of
chemical shift tensors.
RESEt: Reset the assigned energy potentials
PRINt ANALysis: dump out junk data from the potentials
File: SSNMR, Node: 15N Chemical shift : Charmm input, Up: Top, Next: 15N-1H dipolar coupling: Syntax, Previous: 15N Chemical shift : Syntax
!----------CHARMM input--------------------------------------------------
! assign the experimental observables
set csexp8 76.50000
set csexp9 85.40000
set csexp10 72.60000
!set chemical shift force constant (kcal/mol/ppm^2)
set csforc 0.5
!generate chemical shift potential
ccs
exps s11 64.0 s22 77.0 s33 217.0 phi 107
assign sele ( resid 8 .and. ( type N .or. type HN )) .or. ( resid 7 .and. ( type C )) end -
forc @csforc exp @csexp8
assign sele ( resid 9 .and. ( type N .or. type HN )) .or. ( resid 8 .and. ( type C )) end -
forc @csforc exp @csexp9
assign sele ( resid 10 .and. ( type N .or. type HN )) .or. ( resid 9 .and. ( type C )) end -
forc @csforc exp @csexp10
end
!dump out junk data from the assigned potentials
ccs
print anal
end
!get total energy
energy
!test first
test first sele ires 8:45 .and. (type N .or. type HN .or. type C) end
stop
!------------------------------------------------------------------------
File: SSNMR, Node: 15N-1H dipolar coupling: Syntax, Up: Top, Next: 15N-1H dipolar coupling : Charmm input, Previous: 15N Chemical shift : Charmm input
2. 15N-1H dipolar coupling (any dipolar couplings are possible, such as 13C-1H
and etc.)
[Syntax]
CCS
EXPS [NUDC real] DCABs DIPC
ASSIGN atom-selection [FORCe real] [EXP real]
RESEt
PRINt ANALysis
END
NUDC: Dipolar coupling constant; the value depends on the length of
dipolar coupling vector (NH); in the case of NH vector length
(1.07 Angstrom), it is ~19.86 kHz. If you want the simulation
to be flexible dipolar coupling constant, use the keyword DCABs.
DCABs: Flexible dipolar coupling constant will be used in the
simulation.
DIPC: It lets CHARMM to know the assingment to be dipolar coupling.
FORCe: Force constant (unit: kcal/mol/kHz^2).
EXP: Dipolar coupling observables from experiment (kHz).
atom-selection: Two atoms ( N/HN, CA/HA,and etc.) consisting of dipolar
coupling.
RESEt: Reset the assigned energy potentials
PRINt ANALysis: dump out junk data from the potentials
File: SSNMR, Node: 15N-1H dipolar coupling : Charmm input, Up: Top, Next:, Previous: 15N-1H dipolar coupling: Syntax
!----------CHARMM input--------------------------------------------------
! assign the experimental observables
set dcexp7 -9.26125
set dcexp8 -11.09568
set dcexp9 -8.12626
!set dipolar coupling force constant (kcal/mol/kHz^2)
set dcforc 0.5
!generate dipolar coupling potential
ccs
exps nudc 19.86 ! DCABs
!DC
assign sele ( resid 7 .and. ( type N .or. type HN )) end -
DIPC forc @dcforc exp @dcexp7
assign sele ( resid 8 .and. ( type N .or. type HN )) end -
DIPC forc @dcforc exp @dcexp8
assign sele ( resid 9 .and. ( type N .or. type HN )) end -
DIPC forc @dcforc exp @dcexp9
end
!dump out junk data from the assigned potentials
ccs
print anal
end
!get total energy
energy
!test first
test first tol 0.000000001 sele ires 7:45 .and. ( type N .or. type HN ) end
stop
!------------------------------------------------------------------------
This module makes the SSNMR energy functions satisfying experimental data
observed in solid-state NMR. It focuses on 15N-chemical shifts and 15N-1H
dipolar couplings in a solid state. A set of these energy potentials are called
as orientational restraints providing us with the orientation information, such
as tilt, rotation, and etc. of in a particular helix. The module is specialized
on determining helix orientations in a bilayer.
Please report problems to mack97hyuk@gmail.com or wonpil@ku.edu
References : J. Lee, J. Chen, C. L. Brooks III, and W. Im,
J. Magn. Reson. 193, 68-76(2008)
: it includes the explanation of developement and application for
these restraints.
* 15N Chemical shift : Syntax :: Syntax of 15N chemical shift
* 15N Cheimical shift : Charmm input :: Example of 15N chemical shift
* 15N-1H dipolar coupling: Syntax :: Syntax of 15N-1H dipolar coupling
* 15N-1H dipolar coupling: Charmm input :: Example of 15N-1H dipolar coupling
File: SSNMR, Node: 15N Chemical shift : Syntax, Up: Top, Next: 15N Chemical shift : Charmm input, Previous: Top
1. 15N chemical shift
[SYNTAX]
CCS
EXPS [S11 real] [S22 real] [S33 real] [PHI real]
ASSIGN atom-selection [FORCe real] [EXP real]
RESEt
PRINt ANALysis
END
S11, S22, S33: Chemical shift tensors (ppm). They are obtained by diagonalizing
a shielding tensor. These values are given from experiments.
Refer Table1 in the above reference.
PHI: Phi angle (degrees) is defined by a rotation angle between NH
vector and S11 chemical tensor on the peptide plane. It depends
on the residues and also experimental conditions.
FORCe: Force constant (unit: kcal/mol/ppm^2).
EXP: Chemical shift observables from experiment (ppm).
atom-selection: Three atoms (NH, C, and O in peptide plane) consisting of
chemical shift tensors.
RESEt: Reset the assigned energy potentials
PRINt ANALysis: dump out junk data from the potentials
File: SSNMR, Node: 15N Chemical shift : Charmm input, Up: Top, Next: 15N-1H dipolar coupling: Syntax, Previous: 15N Chemical shift : Syntax
!----------CHARMM input--------------------------------------------------
! assign the experimental observables
set csexp8 76.50000
set csexp9 85.40000
set csexp10 72.60000
!set chemical shift force constant (kcal/mol/ppm^2)
set csforc 0.5
!generate chemical shift potential
ccs
exps s11 64.0 s22 77.0 s33 217.0 phi 107
assign sele ( resid 8 .and. ( type N .or. type HN )) .or. ( resid 7 .and. ( type C )) end -
forc @csforc exp @csexp8
assign sele ( resid 9 .and. ( type N .or. type HN )) .or. ( resid 8 .and. ( type C )) end -
forc @csforc exp @csexp9
assign sele ( resid 10 .and. ( type N .or. type HN )) .or. ( resid 9 .and. ( type C )) end -
forc @csforc exp @csexp10
end
!dump out junk data from the assigned potentials
ccs
print anal
end
!get total energy
energy
!test first
test first sele ires 8:45 .and. (type N .or. type HN .or. type C) end
stop
!------------------------------------------------------------------------
File: SSNMR, Node: 15N-1H dipolar coupling: Syntax, Up: Top, Next: 15N-1H dipolar coupling : Charmm input, Previous: 15N Chemical shift : Charmm input
2. 15N-1H dipolar coupling (any dipolar couplings are possible, such as 13C-1H
and etc.)
[Syntax]
CCS
EXPS [NUDC real] DCABs DIPC
ASSIGN atom-selection [FORCe real] [EXP real]
RESEt
PRINt ANALysis
END
NUDC: Dipolar coupling constant; the value depends on the length of
dipolar coupling vector (NH); in the case of NH vector length
(1.07 Angstrom), it is ~19.86 kHz. If you want the simulation
to be flexible dipolar coupling constant, use the keyword DCABs.
DCABs: Flexible dipolar coupling constant will be used in the
simulation.
DIPC: It lets CHARMM to know the assingment to be dipolar coupling.
FORCe: Force constant (unit: kcal/mol/kHz^2).
EXP: Dipolar coupling observables from experiment (kHz).
atom-selection: Two atoms ( N/HN, CA/HA,and etc.) consisting of dipolar
coupling.
RESEt: Reset the assigned energy potentials
PRINt ANALysis: dump out junk data from the potentials
File: SSNMR, Node: 15N-1H dipolar coupling : Charmm input, Up: Top, Next:, Previous: 15N-1H dipolar coupling: Syntax
!----------CHARMM input--------------------------------------------------
! assign the experimental observables
set dcexp7 -9.26125
set dcexp8 -11.09568
set dcexp9 -8.12626
!set dipolar coupling force constant (kcal/mol/kHz^2)
set dcforc 0.5
!generate dipolar coupling potential
ccs
exps nudc 19.86 ! DCABs
!DC
assign sele ( resid 7 .and. ( type N .or. type HN )) end -
DIPC forc @dcforc exp @dcexp7
assign sele ( resid 8 .and. ( type N .or. type HN )) end -
DIPC forc @dcforc exp @dcexp8
assign sele ( resid 9 .and. ( type N .or. type HN )) end -
DIPC forc @dcforc exp @dcexp9
end
!dump out junk data from the assigned potentials
ccs
print anal
end
!get total energy
energy
!test first
test first tol 0.000000001 sele ires 7:45 .and. ( type N .or. type HN ) end
stop
!------------------------------------------------------------------------