c42b1

gopair

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
Top [INPUT GoPair command] GOPAIR [READ UNIT integer] [ON/OFF] [CLEAR] [ETEN ON/OFF]
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.
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.