Mon Oct 10 09:45:57 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 09:45:57 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5803338 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -17.75400 36.31700 ymin,ymax (A): -62.93400 -5.506000 zmin,zma (A): -3.921000 57.42300 x,y,z range (A): 54.07100 57.42800 61.34400 scale (grids/A): 0.5803338 object centre (A): 9.281499 -34.22000 26.75100 number of atom coordinates read : 2859 total number of charged atoms : 2706 net assigned charge : 4.014014 assigned positive charge : 419.9719 centred at (gu) : 89.58996 88.96877 87.02975 assigned negative charge : -415.9583 centred at (gu) : 89.68859 88.86936 86.94905 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6423 nv = 96 ne = 84 npr = 56532 no. pairs analyzed = 56532 no. exposed pairs = 4381 no. arc points = 31327 no. surface atoms = 1437 nbur = 1422 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 337 mr = 2787 m= 0 mr = 11 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3962 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3108 ## 351 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5572635E-09 1.3090724E-09 midg,1,midg; midg,igrid,midg -1.4460686E-09 2.3342113E-09 1,midg,midg; igrid,midg,midg 3.2520535E-09 -9.9573993E-10 gauss-seidel spectral radius is 0.9846787 estimated iterations to convergence 66 setup time was (sec) 0.6300000 now iterating at: 09:45:58 rms-change max change #iterations 9.5778868E-02 17.45321 at 10iterations 7.5885607E-03 1.149036 at 20iterations 6.1381917E-04 9.8583221E-02 at 30iterations 7.0532376E-05 1.1634827E-02 at 40iterations 1.4284035E-05 2.4299622E-03 at 50iterations finished qdiffx linear iterations at : 09:46:01 total time elapsed so far: 3.910000 # loops : 50 mean,max change (kT/e) : 1.4284035E-05 2.4299622E-03 energy calculations done at 3.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 09:46:01 4.094u 0.263s 0:04.64 93.7% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 09:46:02 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.741001 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -17.75400 36.31700 ymin,ymax (A): -62.93400 -5.506000 zmin,zma (A): -3.921000 57.42300 x,y,z range (A): 54.07100 57.42800 61.34400 scale (grids/A): 1.741001 object centre (A): 9.281499 -34.22000 26.75100 number of atom coordinates read : 2859 total number of charged atoms : 2706 net assigned charge : 4.014014 assigned positive charge : 419.9719 centred at (gu) : 88.76954 86.90588 81.08875 assigned negative charge : -415.9583 centred at (gu) : 89.06552 86.60785 80.84711 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 67812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31327 grid for indexing accessible points = 1.400000 m= 21903 mr = 41097 m= 2999 mr = 13765 m= 137 mr = 1381 m= 0 mr = 22 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 36586 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 258 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21056 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5803338 object centre at (A) : 9.281499 -34.22000 26.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4457828E-03 5.5013467E-03 midg,1,midg; midg,igrid,midg 1.5403833E-02 2.7055912E-02 1,midg,midg; igrid,midg,midg 1.4434807E-02 9.6105654E-03 gauss-seidel spectral radius is 0.9984099 estimated iterations to convergence 199 setup time was (sec) 0.9400000 now iterating at: 09:46:03 rms-change max change #iterations 3.707158 163.1773 at 10iterations 1.630255 63.13959 at 20iterations 0.7134974 25.34572 at 30iterations 0.3134546 11.29794 at 40iterations 0.1374875 5.195110 at 50iterations 6.0346663E-02 2.464563 at 60iterations 2.6622802E-02 0.9916229 at 70iterations 1.1680924E-02 0.4933186 at 80iterations 5.1612672E-03 0.1829224 at 90iterations 2.2682594E-03 8.4257126E-02 at 100iterations 1.0046948E-03 3.5795212E-02 at 110iterations 4.4176364E-04 1.6172886E-02 at 120iterations finished qdiffx linear iterations at : 09:46:11 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 4.4176364E-04 1.6172886E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 09:46:12 9.418u 0.294s 0:10.01 96.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 09:46:12 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.611502 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -17.75400 36.31700 ymin,ymax (A): -62.93400 -5.506000 zmin,zma (A): -3.921000 57.42300 x,y,z range (A): 54.07100 57.42800 61.34400 scale (grids/A): 2.611502 object centre (A): 9.281499 -34.22000 26.75100 number of atom coordinates read : 2859 total number of charged atoms : 2706 net assigned charge : 4.014014 assigned positive charge : 419.9719 centred at (gu) : 88.15422 85.35850 76.63307 assigned negative charge : -415.9583 centred at (gu) : 88.59813 84.91181 76.27061 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 156313 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31327 grid for indexing accessible points = 1.400000 m= 71112 mr = 101436 m= 24057 mr = 52379 m= 4841 mr = 17205 m= 451 mr = 2981 m= 16 mr = 203 m= 0 mr = 6 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 82580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 21640 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.741001 object centre at (A) : 9.281499 -34.22000 26.75100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1160513E-02 0.1093548 midg,1,midg; midg,igrid,midg 0.4640725 0.3410095 1,midg,midg; igrid,midg,midg 0.1213857 0.1588979 gauss-seidel spectral radius is 0.9992201 estimated iterations to convergence 283 setup time was (sec) 1.940000 now iterating at: 09:46:14 rms-change max change #iterations 9.609995 267.6981 at 10iterations 5.689147 152.7298 at 20iterations 3.324435 115.2510 at 30iterations 1.930483 60.69733 at 40iterations 1.111195 26.50300 at 50iterations 0.6382207 21.55956 at 60iterations 0.3654734 9.317062 at 70iterations 0.2087347 4.853355 at 80iterations 0.1190053 2.677994 at 90iterations 6.7842096E-02 1.479799 at 100iterations 3.8643461E-02 0.8898787 at 110iterations 2.1977553E-02 0.5336232 at 120iterations 1.2486479E-02 0.2881942 at 130iterations 7.0769456E-03 0.1509876 at 140iterations 4.0192232E-03 9.0618134E-02 at 150iterations 2.2859264E-03 4.8755646E-02 at 160iterations 1.2978991E-03 2.8619766E-02 at 170iterations 7.3760713E-04 1.4883056E-02 at 180iterations finished qdiffx linear iterations at : 09:46:28 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 7.3760713E-04 1.4883056E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.86000 DelPhi exited at 09:46:28 15.864u 0.297s 0:16.43 98.2% 0+0k 0+0io 0pf+0w