gopair (c41b2)
The Go pairwise Energy Module of CHARMM
By Charles L. Brooks III, 2014
The Go Pair facility in CHARMM was added to complement and extend the
functionality of the Karinoclas and Brooks Go model implementation in
protein/nucleic chains are treated as KB-specific Go models and the
inter-chain interactions are modeled as either KB-like Go interactions
or some generaic form of coarse-grained interaction model, e.g., if
one wants to consider the interactions of two proteins of known
structure, for which one can build a KB Go model, and have the
inter-chain/protein interactions occur with a general Mizawa-Jernigan
pairwise Ca-based interaction. In this case, the GoPair facility
accounts for the non-generic intra-protein/chain interactions via the
pairwise modified MJ KB Go interactions and the generic repulsive
terms within the chain are treated via the normal non-bonded routines
as are the inter-chain interactions.
Note: In this implementation the intra-chain KB-based Go interactions
are not subject to periodic boundary conditions and all pairwise
interactions are considered, i.e., no cutoffs. Whereas, the
non-Go/non-specific interactions are treated via periodic boundary
conditions with cutoffs.
The ETEN functionality is available and can be turned on or off
independently from that govering the non-specific pairwise
interactions. Thus one can do "mixed" models where intra-protein
interactions are treated with the KB form and inter-chain are treated
with standard LJ, or visa-versa (remember, the replusive intra-chain
interactions are treated via the normal ETEN ON/OFF model here.
How it works
------------
The Go Pair functionality reads a list of pairwise interaction
parameters, i.e., emin and rmin ananlgous to the NBFIX pairwise
parameters, and sets up the list structure to calculate the energy and
forces on the specified pairs using the specified functional form
(ETEN ON/OFF). These pairwise interactions are put on the non-bonded
exclusion list so they are not double counted. In doing so, as noted
above, the set of pairwise interactions specified by the GOPAIR
commands ARE NOT SUBJECT TO CUTOFFS OR PEREIODIC BOUNDARY CONDITIONS,
and hence are only appropriate for single chains or multi-chain
systems that are confied by some means other than periodic boundary
conditions.
References:
(1) Karanicolas & Brooks, Protein Science, 11, 2351 (2002).
* Syntax | Syntax of the GoPair command
* Function | Purpose of each of the keywords
* Example | Example input setup
By Charles L. Brooks III, 2014
The Go Pair facility in CHARMM was added to complement and extend the
functionality of the Karinoclas and Brooks Go model implementation in
protein/nucleic chains are treated as KB-specific Go models and the
inter-chain interactions are modeled as either KB-like Go interactions
or some generaic form of coarse-grained interaction model, e.g., if
one wants to consider the interactions of two proteins of known
structure, for which one can build a KB Go model, and have the
inter-chain/protein interactions occur with a general Mizawa-Jernigan
pairwise Ca-based interaction. In this case, the GoPair facility
accounts for the non-generic intra-protein/chain interactions via the
pairwise modified MJ KB Go interactions and the generic repulsive
terms within the chain are treated via the normal non-bonded routines
as are the inter-chain interactions.
Note: In this implementation the intra-chain KB-based Go interactions
are not subject to periodic boundary conditions and all pairwise
interactions are considered, i.e., no cutoffs. Whereas, the
non-Go/non-specific interactions are treated via periodic boundary
conditions with cutoffs.
The ETEN functionality is available and can be turned on or off
independently from that govering the non-specific pairwise
interactions. Thus one can do "mixed" models where intra-protein
interactions are treated with the KB form and inter-chain are treated
with standard LJ, or visa-versa (remember, the replusive intra-chain
interactions are treated via the normal ETEN ON/OFF model here.
How it works
------------
The Go Pair functionality reads a list of pairwise interaction
parameters, i.e., emin and rmin ananlgous to the NBFIX pairwise
parameters, and sets up the list structure to calculate the energy and
forces on the specified pairs using the specified functional form
(ETEN ON/OFF). These pairwise interactions are put on the non-bonded
exclusion list so they are not double counted. In doing so, as noted
above, the set of pairwise interactions specified by the GOPAIR
commands ARE NOT SUBJECT TO CUTOFFS OR PEREIODIC BOUNDARY CONDITIONS,
and hence are only appropriate for single chains or multi-chain
systems that are confied by some means other than periodic boundary
conditions.
References:
(1) Karanicolas & Brooks, Protein Science, 11, 2351 (2002).
* Syntax | Syntax of the GoPair command
* Function | Purpose of each of the keywords
* Example | Example input setup
Top
READ : Read the Go-model pairwise interactions from unit <integer>,
default is to read from input stream
ON/OFF : Turn the Go Pair functionality on or off (note reading the
parameters automatically turns it on and clearing the
data structures automativally turns it off.
CLEAr : Turn off GoPair functionality and delete data structures
ETEN : Turns the KB ETEN functional form on <ON> or off <OFF>.
Default is ETEN OFF.
PBC : Turns on GoPair PBC (with minimum image convention) calculation
for pair distances specified in Go Pair list from READ.
NOTE: This is only implemented for rhombahedral volumes, i.e.,
alpha=beta=gamma=90. Also, only a simple stuncation at CTOFNB
is performed.
READ : Read the Go-model pairwise interactions from unit <integer>,
default is to read from input stream
ON/OFF : Turn the Go Pair functionality on or off (note reading the
parameters automatically turns it on and clearing the
data structures automativally turns it off.
CLEAr : Turn off GoPair functionality and delete data structures
ETEN : Turns the KB ETEN functional form on <ON> or off <OFF>.
Default is ETEN OFF.
PBC : Turns on GoPair PBC (with minimum image convention) calculation
for pair distances specified in Go Pair list from READ.
NOTE: This is only implemented for rhombahedral volumes, i.e.,
alpha=beta=gamma=90. Also, only a simple stuncation at CTOFNB
is performed.
Top
Example usage
-------------
Consider a system comprised of two chains (A & B) for which a standard
KB Go model has been constructed for each chain A and chain B (Note:
in the near future the Go Server will produce an additional file for
the GoPair intrachain interactions separately to facilitate usage of
the GoPair modeling facility, let's assume it's called
model_kb-gopair.param.) and the "generic" intra-chain repulsive
interactions, the generic Mizawa-Jernigan or otherwise determined
inter-chain non-bonded parameters (specified as NBFIXes for the
N_A*(N_B-1)/2 pairs of interacting sites), the "standard" NBFIX KB
parameters for intra-chain A-A and B-B, bonded, angle and torsion
parameters are contained in the parameter file model_kb-go.param. The
topology is described in model_kb-go.top and the initial Ca-only
structures are in model_a.pdb and model_b.pdb.
Files assumed: model_kb-go.top - contains the required topology information
model_kb-go.param - contains the associated parameters
model_a.pdv, model_b.pdb - contains coordinates for chains
A and B.
model_kb-gopair.param - contains the intra-chain non-bonded
KB Go parameters.
***************
model_kb-go.top:
* Topology for Go model of 1arr
20 1
MASS 1 A1 131.000000
MASS 2 A2 128.000000
MASS 3 A3 57.000000
.
.
.
MASS 103 B50 157.000000
MASS 104 B51 113.000000
MASS 105 B52 57.000000
MASS 106 B53 71.000000
DECL +CA
AUTOGENERATE ANGLE DIHEDRAL
RESI A1 0.0
GROU
Atom CA A1 0.0
Bond CA +CA
RESI A2 0.0
GROU
Atom CA A2 0.0
Bond CA +CA
.
.
.
RESI B52 0.0
GROU
Atom CA B52 0.0
Bond CA +CA
RESI B53 0.0
GROU
Atom CA B53 0.0
Bond CA +CA
END
*****************
model_kb-go.param:
* Parameters for Go model of 1arr
BOND
A1 A2 378.000000 3.841480
A2 A3 378.000000 3.832207
.
.
.
B50 B51 378.000000 3.817184
B51 B52 378.000000 3.740986
B52 B53 378.000000 3.807921
ANGLE
A1 A2 A3 75.600000 87.002943
A2 A3 A4 75.600000 92.769692
.
.
.
B49 B50 B51 75.600000 81.795665
B50 B51 B52 75.600000 100.811114
B51 B52 B53 75.600000 98.404340
DIHEDRAL
A1 A2 A3 A4 0.070661 1 148.427948
A1 A2 A3 A4 0.642645 2 247.750476
A1 A2 A3 A4 0.131763 3 98.732133
A1 A2 A3 A4 0.076565 4 20.955060
A2 A3 A4 A5 0.155810 1 253.803724
A2 A3 A4 A5 0.433367 2 21.748974
A2 A3 A4 A5 0.116055 3 221.349291
A2 A3 A4 A5 0.169406 4 13.133496
.
.
.
B50 B51 B52 B53 0.083619 1 189.775808
B50 B51 B52 B53 0.746189 2 228.220978
B50 B51 B52 B53 0.184920 3 106.554957
B50 B51 B52 B53 0.071306 4 353.723408
NONBONDED NBXMOD 3 ATOM CDIEL SWITCH VATOM VDISTANCE VSWITCH -
CUTNB 399.0 CTOFNB 398.5 CTONNB 395.5 EPS 1.0 WMIN 1.5
A1 0.0 -0.000546 2.474456 !The following are generic repulsive
A2 0.0 -0.000012 4.738648 ! interactions beween atoms.
A3 0.0 -0.000224 6.214139
.
.
.
B50 0.0 -0.000155 3.489662
B51 0.0 -0.000654 2.905577
B52 0.0 -0.000224 3.193040
B53 0.0 -0.000272 4.391179
NBFIX
A1 A4 -2.36758 3.843863 ! These are the intra-chain KB Go
A1 A6 -0.924458 4.937081 ! parameters for chain A
A2 A5 -0.391404 6.159995
A14 A18 -2.522816 6.612486
.
.
.
B1 B4 -2.36758 3.843863 ! These are the intra-chain KB Go
B1 B6 -0.924458 4.937081 ! parameters for chain B
B2 B5 -0.391404 6.159995
B14 B18 -2.522816 6.612486
B14 B19 -2.288776 6.526276
.
.
.
A1 B1 -0.257896 8.490313 ! These are the generic MJ non-bonded
A1 B2 -0.117140 8.439674 ! parameters for all N_A*(N_B-1)/2
A1 B3 -0.160122 4.500000 ! pairs of interactions.
A1 B4 -0.257896 8.490313
.
.
.
A53 B47 -0.061876 6.957982
A53 B48 -0.071323 6.762163
A53 B49 -0.109110 4.500000
A53 B50 -0.086438 7.992829
A53 B51 -0.216330 6.743982
A53 B52 -0.109110 4.500000
A53 B53 -0.128476 5.530169
END
**********************
model_kb-gopair.param:
198 bynu ! Note this format specifies atom pair selection by number (bynu)
1 4 -2.36758 3.843863 ! This specfies atom 1 and atom 4 emin and rmin.
1 6 -0.924458 4.937081 ! These are the same as the intrachain NBFIXes
2 5 -0.391404 6.159995 ! in the model_kb-go.param file.
.
.
.
102 105 -2.36758 6.726333
102 106 -1.775686 6.685909
103 106 -0.68216 5.186839
Note: there are 53 residues (Ca atoms in each chain, thus 106 total atoms.
There is an alternative form for specifying the pairwise interactions in
this file, where specific atom selection syntax is used.
**********************************
Alternative model_kb-gopair.param:
198 ! Note that there is no bynu here so full selection syntax below.
sele bynu 1 end sele bynu 4 end -2.36758 3.843863
sele bynu 1 end sele bynu 6 end -0.924458 4.937081
sele bynu 2 end sele bynu 5 end -0.391404 6.159995
.
.
.
sele bynu 102 end sele bynu 105 end -2.36758 6.726333
sele bynu 102 end sele bynu 106 end -1.775686 6.685909
sele bynu 103 end sele bynu 106 end -0.68216 5.186839
*********************
Example input stream:
The following CHARMM command script provides an example of
setting up energy calculations using the Go Pair facility.
* Test input script for model system 1arr
* dimer represented by a mixed KB-Go/MJ interaction
* model.
! Read the general RTF and parameter files
read rtf card name model_kb-go.top
read param card name model_kb-go.param
! Set-up the PSF by reading sequence, generating and
! reading coordinates for each chain.
read sequ pdb name go_a.pdb
generate proa autogenerate angle dihedral
read coor pdb name go_a.pdb
read sequ pdb name go_b.pdb
generate prob autogenerate angle dihedral
read coor pdb name go_b.pdb
! Turn on periodic boundary conditions using
! images for a cubic volume
set boxsize = 120
read image card
* IMAGE FILE FOR CUBIC TRANSFORMATION
* BOX SIZE IS @boxsize X @boxsize X @boxsize ANGSTROMS
SCALE @boxsize @boxsize @boxsize
IMAGE X
TRANS 1.0 0.0 0.0
IMAGE A
TRANS -1.0 0.0 0.0
IMAGE XY
TRANS 1.0 1.0 0.0
.
.
.
IMAGE XBC
TRANS 1.0 -1.0 -1.0
IMAGE BC
TRANS 0.0 -1.0 -1.0
IMAGE ABC
TRANS -1.0 -1.0 -1.0
END
IMAGE BYSEGID XCEN 0.0 YCEN 0.0 ZCEN 0.0
! We will use the ETEN model in this section
eten on
energy cutnb 25 ctonnb 25 ctofnb 25 cutim 25
set e_kbgo = ?ener ! Set energy variable for later comparison
! Now set-up GoPair model
open unit 1 read form name model_kb-gopair.param
gopair read unit 1 eten on
update ! doing update here ensures that exclusion list is built
energy
set e_gopair = ?ener
calc diff = abs ( @e_kbgo - @e_gopair ) ! value of diff should be zero
! Now turn gopair off and calculate energy, should match @e_kbgo
gopair off
update ! rebuild corrected exclusion list
energy
calc diff = abs ( @e_kbgo - ?ener ) ! Again, this should be 0.
! Turn GoPair back on and check
gopair on
update
energy
calc diff = abs ( @e_kbgo - ?ener ) ! Again, this should be 0.
! Now turn off gopair and switch to ETEN OFF
gopair off
eten off
update
energy
set e_kbgo = ?ener
gopair on eten off
update
energy
set e_gopair = ?ener
calc diff = abs ( @e_kbgo - @e_gopair ) ! value of diff should be zero
stop
From here one may move on to do dynamics or any of the other molecular
mechanics manipulations with the GoPair model.
Example usage
-------------
Consider a system comprised of two chains (A & B) for which a standard
KB Go model has been constructed for each chain A and chain B (Note:
in the near future the Go Server will produce an additional file for
the GoPair intrachain interactions separately to facilitate usage of
the GoPair modeling facility, let's assume it's called
model_kb-gopair.param.) and the "generic" intra-chain repulsive
interactions, the generic Mizawa-Jernigan or otherwise determined
inter-chain non-bonded parameters (specified as NBFIXes for the
N_A*(N_B-1)/2 pairs of interacting sites), the "standard" NBFIX KB
parameters for intra-chain A-A and B-B, bonded, angle and torsion
parameters are contained in the parameter file model_kb-go.param. The
topology is described in model_kb-go.top and the initial Ca-only
structures are in model_a.pdb and model_b.pdb.
Files assumed: model_kb-go.top - contains the required topology information
model_kb-go.param - contains the associated parameters
model_a.pdv, model_b.pdb - contains coordinates for chains
A and B.
model_kb-gopair.param - contains the intra-chain non-bonded
KB Go parameters.
***************
model_kb-go.top:
* Topology for Go model of 1arr
20 1
MASS 1 A1 131.000000
MASS 2 A2 128.000000
MASS 3 A3 57.000000
.
.
.
MASS 103 B50 157.000000
MASS 104 B51 113.000000
MASS 105 B52 57.000000
MASS 106 B53 71.000000
DECL +CA
AUTOGENERATE ANGLE DIHEDRAL
RESI A1 0.0
GROU
Atom CA A1 0.0
Bond CA +CA
RESI A2 0.0
GROU
Atom CA A2 0.0
Bond CA +CA
.
.
.
RESI B52 0.0
GROU
Atom CA B52 0.0
Bond CA +CA
RESI B53 0.0
GROU
Atom CA B53 0.0
Bond CA +CA
END
*****************
model_kb-go.param:
* Parameters for Go model of 1arr
BOND
A1 A2 378.000000 3.841480
A2 A3 378.000000 3.832207
.
.
.
B50 B51 378.000000 3.817184
B51 B52 378.000000 3.740986
B52 B53 378.000000 3.807921
ANGLE
A1 A2 A3 75.600000 87.002943
A2 A3 A4 75.600000 92.769692
.
.
.
B49 B50 B51 75.600000 81.795665
B50 B51 B52 75.600000 100.811114
B51 B52 B53 75.600000 98.404340
DIHEDRAL
A1 A2 A3 A4 0.070661 1 148.427948
A1 A2 A3 A4 0.642645 2 247.750476
A1 A2 A3 A4 0.131763 3 98.732133
A1 A2 A3 A4 0.076565 4 20.955060
A2 A3 A4 A5 0.155810 1 253.803724
A2 A3 A4 A5 0.433367 2 21.748974
A2 A3 A4 A5 0.116055 3 221.349291
A2 A3 A4 A5 0.169406 4 13.133496
.
.
.
B50 B51 B52 B53 0.083619 1 189.775808
B50 B51 B52 B53 0.746189 2 228.220978
B50 B51 B52 B53 0.184920 3 106.554957
B50 B51 B52 B53 0.071306 4 353.723408
NONBONDED NBXMOD 3 ATOM CDIEL SWITCH VATOM VDISTANCE VSWITCH -
CUTNB 399.0 CTOFNB 398.5 CTONNB 395.5 EPS 1.0 WMIN 1.5
A1 0.0 -0.000546 2.474456 !The following are generic repulsive
A2 0.0 -0.000012 4.738648 ! interactions beween atoms.
A3 0.0 -0.000224 6.214139
.
.
.
B50 0.0 -0.000155 3.489662
B51 0.0 -0.000654 2.905577
B52 0.0 -0.000224 3.193040
B53 0.0 -0.000272 4.391179
NBFIX
A1 A4 -2.36758 3.843863 ! These are the intra-chain KB Go
A1 A6 -0.924458 4.937081 ! parameters for chain A
A2 A5 -0.391404 6.159995
A14 A18 -2.522816 6.612486
.
.
.
B1 B4 -2.36758 3.843863 ! These are the intra-chain KB Go
B1 B6 -0.924458 4.937081 ! parameters for chain B
B2 B5 -0.391404 6.159995
B14 B18 -2.522816 6.612486
B14 B19 -2.288776 6.526276
.
.
.
A1 B1 -0.257896 8.490313 ! These are the generic MJ non-bonded
A1 B2 -0.117140 8.439674 ! parameters for all N_A*(N_B-1)/2
A1 B3 -0.160122 4.500000 ! pairs of interactions.
A1 B4 -0.257896 8.490313
.
.
.
A53 B47 -0.061876 6.957982
A53 B48 -0.071323 6.762163
A53 B49 -0.109110 4.500000
A53 B50 -0.086438 7.992829
A53 B51 -0.216330 6.743982
A53 B52 -0.109110 4.500000
A53 B53 -0.128476 5.530169
END
**********************
model_kb-gopair.param:
198 bynu ! Note this format specifies atom pair selection by number (bynu)
1 4 -2.36758 3.843863 ! This specfies atom 1 and atom 4 emin and rmin.
1 6 -0.924458 4.937081 ! These are the same as the intrachain NBFIXes
2 5 -0.391404 6.159995 ! in the model_kb-go.param file.
.
.
.
102 105 -2.36758 6.726333
102 106 -1.775686 6.685909
103 106 -0.68216 5.186839
Note: there are 53 residues (Ca atoms in each chain, thus 106 total atoms.
There is an alternative form for specifying the pairwise interactions in
this file, where specific atom selection syntax is used.
**********************************
Alternative model_kb-gopair.param:
198 ! Note that there is no bynu here so full selection syntax below.
sele bynu 1 end sele bynu 4 end -2.36758 3.843863
sele bynu 1 end sele bynu 6 end -0.924458 4.937081
sele bynu 2 end sele bynu 5 end -0.391404 6.159995
.
.
.
sele bynu 102 end sele bynu 105 end -2.36758 6.726333
sele bynu 102 end sele bynu 106 end -1.775686 6.685909
sele bynu 103 end sele bynu 106 end -0.68216 5.186839
*********************
Example input stream:
The following CHARMM command script provides an example of
setting up energy calculations using the Go Pair facility.
* Test input script for model system 1arr
* dimer represented by a mixed KB-Go/MJ interaction
* model.
! Read the general RTF and parameter files
read rtf card name model_kb-go.top
read param card name model_kb-go.param
! Set-up the PSF by reading sequence, generating and
! reading coordinates for each chain.
read sequ pdb name go_a.pdb
generate proa autogenerate angle dihedral
read coor pdb name go_a.pdb
read sequ pdb name go_b.pdb
generate prob autogenerate angle dihedral
read coor pdb name go_b.pdb
! Turn on periodic boundary conditions using
! images for a cubic volume
set boxsize = 120
read image card
* IMAGE FILE FOR CUBIC TRANSFORMATION
* BOX SIZE IS @boxsize X @boxsize X @boxsize ANGSTROMS
SCALE @boxsize @boxsize @boxsize
IMAGE X
TRANS 1.0 0.0 0.0
IMAGE A
TRANS -1.0 0.0 0.0
IMAGE XY
TRANS 1.0 1.0 0.0
.
.
.
IMAGE XBC
TRANS 1.0 -1.0 -1.0
IMAGE BC
TRANS 0.0 -1.0 -1.0
IMAGE ABC
TRANS -1.0 -1.0 -1.0
END
IMAGE BYSEGID XCEN 0.0 YCEN 0.0 ZCEN 0.0
! We will use the ETEN model in this section
eten on
energy cutnb 25 ctonnb 25 ctofnb 25 cutim 25
set e_kbgo = ?ener ! Set energy variable for later comparison
! Now set-up GoPair model
open unit 1 read form name model_kb-gopair.param
gopair read unit 1 eten on
update ! doing update here ensures that exclusion list is built
energy
set e_gopair = ?ener
calc diff = abs ( @e_kbgo - @e_gopair ) ! value of diff should be zero
! Now turn gopair off and calculate energy, should match @e_kbgo
gopair off
update ! rebuild corrected exclusion list
energy
calc diff = abs ( @e_kbgo - ?ener ) ! Again, this should be 0.
! Turn GoPair back on and check
gopair on
update
energy
calc diff = abs ( @e_kbgo - ?ener ) ! Again, this should be 0.
! Now turn off gopair and switch to ETEN OFF
gopair off
eten off
update
energy
set e_kbgo = ?ener
gopair on eten off
update
energy
set e_gopair = ?ener
calc diff = abs ( @e_kbgo - @e_gopair ) ! value of diff should be zero
stop
From here one may move on to do dynamics or any of the other molecular
mechanics manipulations with the GoPair model.