rdc (c49b1)
Residual Dipolar coupling (RDC) module
Residual dipolar coupling (RDC) is an orientational restraint offering
information about the average orientation of an internuclear vector formed
by two NMR active nuclei with respect to the static magnetic field. This
module allows the user to restrain RDC during the NMR structure calculation.
Please report problems to tr@iith.ac.in or wonpil@ku.edu
Reference : Rathinavelani, T. and Im, W., J. Comp. Chem.
28:1858 & 29:1640 (2007)
* Syntax | Syntax of RDC restraint module
* Details | Details of RDC commands
* Example | Examples for RDC restraints
Residual dipolar coupling (RDC) is an orientational restraint offering
information about the average orientation of an internuclear vector formed
by two NMR active nuclei with respect to the static magnetic field. This
module allows the user to restrain RDC during the NMR structure calculation.
Please report problems to tr@iith.ac.in or wonpil@ku.edu
Reference : Rathinavelani, T. and Im, W., J. Comp. Chem.
28:1858 & 29:1640 (2007)
* Syntax | Syntax of RDC restraint module
* Details | Details of RDC commands
* Example | Examples for RDC restraints
Top
Syntax of RDC restraint module
RDC Reset
RDC [MAXRDC integer] [NSET integer] [SRDC] [QRMF] [QFIXA] [QFIXB] [SLOW]
[URDC integer] [BMRB] [XPLOR] [KHAR real] [LHAR real] [KASY real]
[EXPO integer]
RDC Anal [URDC integer]
RDC Bcal [IATM character] [JATM character] [RRES integer] [URDC integer].
______________________________________________________________________
Syntax of RDC restraint module
RDC Reset
RDC [MAXRDC integer] [NSET integer] [SRDC] [QRMF] [QFIXA] [QFIXB] [SLOW]
[URDC integer] [BMRB] [XPLOR] [KHAR real] [LHAR real] [KASY real]
[EXPO integer]
RDC Anal [URDC integer]
RDC Bcal [IATM character] [JATM character] [RRES integer] [URDC integer].
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Top
Details of RDC commands
1 NSET Number of alignment media from which RDCs are collected; Default 1.
2 MAXRDC Maximum number of RDC restraints; Default 1000.
3 SRDC Normalizes (scales) the given RDCs with respect to NH RDC.
4 KHAR Force constant for harmonic restraint; Default 1.
5 LHAR Length of the harmonic function; Default 1.
6 KASY Force constant for the soft asymptotic potential; Default 1.
7 EXPO Exponential function for soft asymptote; Default 1.
8 QRMF Define molecular frame only using RDC atoms.
9 QFIXA Fix the alignment tensor.
10 QFIXB Fix all the RDC bonds.
11 SLOW RDC full force calculation.
12 URDC Unit number of the file from which the RDC data should be read.
13 XPLO XPLOR format RDC input; Default format: CHARMM.
14 BMRB BMRB format RDC input; Default format: CHARMM.
15 ANAL Gives detailed analysis of observed versus calculated RDCs.
16 BCAL Given one type of RDC, for instance HN-H, does the back calculation
of RDCs like CA-HA, C-CA etc using the alignment tensor derived
using HN-N RDC. Requires atoms involved in RDC back calculation.
If the URDC is specified, the output will be stored in a separate
file that has a URDC number as the suffix and prefix as 'fort'.
If URDC is not specified, the analysis will be displayed in the
CHARMM output file itself. RRES indicates the starting residue
number. Note that back calculation of RDC will not work for
methylene RDCs.
17 RESET Resets all assignments of the RDC module.
Details of RDC commands
1 NSET Number of alignment media from which RDCs are collected; Default 1.
2 MAXRDC Maximum number of RDC restraints; Default 1000.
3 SRDC Normalizes (scales) the given RDCs with respect to NH RDC.
4 KHAR Force constant for harmonic restraint; Default 1.
5 LHAR Length of the harmonic function; Default 1.
6 KASY Force constant for the soft asymptotic potential; Default 1.
7 EXPO Exponential function for soft asymptote; Default 1.
8 QRMF Define molecular frame only using RDC atoms.
9 QFIXA Fix the alignment tensor.
10 QFIXB Fix all the RDC bonds.
11 SLOW RDC full force calculation.
12 URDC Unit number of the file from which the RDC data should be read.
13 XPLO XPLOR format RDC input; Default format: CHARMM.
14 BMRB BMRB format RDC input; Default format: CHARMM.
15 ANAL Gives detailed analysis of observed versus calculated RDCs.
16 BCAL Given one type of RDC, for instance HN-H, does the back calculation
of RDCs like CA-HA, C-CA etc using the alignment tensor derived
using HN-N RDC. Requires atoms involved in RDC back calculation.
If the URDC is specified, the output will be stored in a separate
file that has a URDC number as the suffix and prefix as 'fort'.
If URDC is not specified, the analysis will be displayed in the
CHARMM output file itself. RRES indicates the starting residue
number. Note that back calculation of RDC will not work for
methylene RDCs.
17 RESET Resets all assignments of the RDC module.
Top
Examples for RDC restraints
1) Example for reading BMRB format RDC restraints from a file named
data/ubi_rdc.bmrb measured in a single alignment media and restraining
it with soft asymptotic potential parameters KHAR=0.5, KASY=0.5, LHAR=5
and EXPO=1
RDC reset
open read card unit 11 name ubi_rdc.bmrb
RDC KHAR 0.5 KASY 0.5 LHAR 5 EXPO 1 URDC 11 bmrb
2) Example for reading CHARMM format RDC restraints from files protg1.cmm1,
protg1.cmm2, protg1.cmm3, protg1.cmm4 and protg1.cmm5 measured in five
alignment media and restraining it with soft asymptotic potential
parameters KHAR=0.5, KASY=0.5, LHAR=5 and EXPO=1. Different soft asymptotic
potential parameters can be used for different RDCs in the CHAMM format.
RDC reset
set lharmNH = 2.0
set kasymNH = 0.5
set kharmNH = 0.5
set lharmCAC = 2.0
set kasymCAC = 0.5
set kharmCAC = 0.25
set lharmCAH = 2.0
set kasymCAH = 0.25
set kharmCAH = 0.25
set lharmHNC = 2.0
set kasymHNC = 1.0
set kharmHNC = 1.0
set lharmNC = 2.0
set kasymNC = 1.0
set kharmNC = 1.0
open read card unit 11 name protg1.cmm1
open read card unit 12 name protg1.cmm2
open read card unit 13 name protg1.cmm3
open read card unit 14 name protg1.cmm4
open read card unit 15 name protg1.cmm5
RDC nset 5 maxrdc 3000 EXPO 1 URDC 11
Or
RDC nset 5 maxrdc 3000 EXPO 1 URDC 15 URDC 14 URDC 12 URDC 11 URDC 13
3) Example for normalizing RDCs with respect to NH vector as well as to define
the molecular frame with respect to the RDC only atoms.
RDC reset
open read card unit 11 name ubi_rdc.bmrb
RDC SRDC QRMF KHAR 0.5 KASY 0.5 LHAR 5 EXPO 1 URDC 11 bmrb
4) Example for analyzing observed vs calculated RDCs. If the URDC is
specified, the output will be stored in a separate file that has a URDC
number as the suffix and prefix as ".fort". If URDC is not specified,
the analysis will be displayed in the CHARMM output file itself.
To have the analysis details in CHARMM output:
RDC ANAL
To have the analysis details in fort.90:
RDC ANAL URDC 90
5) Example for back calculating RDC from multiple alignment media
To have the analysis details in CHARMM output:
RDC BCAL IATM CA JATM HA
To have the analysis details in CHARMM output, but, with residue number
starting from 20:
RDC BCAL IATM CA JATM HA RRES 20
To have the analysis details in fort.90:
RDC BCAL IATM CA JATM HA URDC 90
Examples for RDC restraints
1) Example for reading BMRB format RDC restraints from a file named
data/ubi_rdc.bmrb measured in a single alignment media and restraining
it with soft asymptotic potential parameters KHAR=0.5, KASY=0.5, LHAR=5
and EXPO=1
RDC reset
open read card unit 11 name ubi_rdc.bmrb
RDC KHAR 0.5 KASY 0.5 LHAR 5 EXPO 1 URDC 11 bmrb
2) Example for reading CHARMM format RDC restraints from files protg1.cmm1,
protg1.cmm2, protg1.cmm3, protg1.cmm4 and protg1.cmm5 measured in five
alignment media and restraining it with soft asymptotic potential
parameters KHAR=0.5, KASY=0.5, LHAR=5 and EXPO=1. Different soft asymptotic
potential parameters can be used for different RDCs in the CHAMM format.
RDC reset
set lharmNH = 2.0
set kasymNH = 0.5
set kharmNH = 0.5
set lharmCAC = 2.0
set kasymCAC = 0.5
set kharmCAC = 0.25
set lharmCAH = 2.0
set kasymCAH = 0.25
set kharmCAH = 0.25
set lharmHNC = 2.0
set kasymHNC = 1.0
set kharmHNC = 1.0
set lharmNC = 2.0
set kasymNC = 1.0
set kharmNC = 1.0
open read card unit 11 name protg1.cmm1
open read card unit 12 name protg1.cmm2
open read card unit 13 name protg1.cmm3
open read card unit 14 name protg1.cmm4
open read card unit 15 name protg1.cmm5
RDC nset 5 maxrdc 3000 EXPO 1 URDC 11
Or
RDC nset 5 maxrdc 3000 EXPO 1 URDC 15 URDC 14 URDC 12 URDC 11 URDC 13
3) Example for normalizing RDCs with respect to NH vector as well as to define
the molecular frame with respect to the RDC only atoms.
RDC reset
open read card unit 11 name ubi_rdc.bmrb
RDC SRDC QRMF KHAR 0.5 KASY 0.5 LHAR 5 EXPO 1 URDC 11 bmrb
4) Example for analyzing observed vs calculated RDCs. If the URDC is
specified, the output will be stored in a separate file that has a URDC
number as the suffix and prefix as ".fort". If URDC is not specified,
the analysis will be displayed in the CHARMM output file itself.
To have the analysis details in CHARMM output:
RDC ANAL
To have the analysis details in fort.90:
RDC ANAL URDC 90
5) Example for back calculating RDC from multiple alignment media
To have the analysis details in CHARMM output:
RDC BCAL IATM CA JATM HA
To have the analysis details in CHARMM output, but, with residue number
starting from 20:
RDC BCAL IATM CA JATM HA RRES 20
To have the analysis details in fort.90:
RDC BCAL IATM CA JATM HA URDC 90