Sat Oct 8 21:42:43 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 Sat Oct 8 2011 at 21:42:43 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6652340 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): 5.639000 59.15400 ymin,ymax (A): 2.665000 49.63000 zmin,zma (A): 14.72500 55.69500 x,y,z range (A): 53.51500 46.96500 40.97000 scale (grids/A): 0.6652340 object centre (A): 32.39650 26.14750 35.21000 number of atom coordinates read : 2028 total number of charged atoms : 1902 net assigned charge : 0.9200045 assigned positive charge : 306.4247 centred at (gu) : 87.71854 89.58521 89.16670 assigned negative charge : -305.5049 centred at (gu) : 87.86408 89.61018 89.16724 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6189 nv = 96 ne = 84 npr = 39882 no. pairs analyzed = 39882 no. exposed pairs = 2690 no. arc points = 18824 no. surface atoms = 907 nbur = 1121 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3340 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1717 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7023 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4852076E-09 1.6342240E-09 midg,1,midg; midg,igrid,midg 6.9946822E-09 -2.2007720E-09 1,midg,midg; igrid,midg,midg 4.4456058E-08 -1.4963055E-08 gauss-seidel spectral radius is 0.9882377 estimated iterations to convergence 75 setup time was (sec) 0.5600000 now iterating at: 21:42:44 rms-change max change #iterations 0.1491960 25.36186 at 10iterations 1.7206673E-02 2.871765 at 20iterations 2.9261236E-03 0.5257339 at 30iterations 9.0725225E-04 0.1893539 at 40iterations 3.3675946E-04 7.0381165E-02 at 50iterations finished qdiffx linear iterations at : 21:42:48 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 3.3675946E-04 7.0381165E-02 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 21:42:48 4.401u 0.385s 0:05.07 94.2% 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 Sat Oct 8 2011 at 21:42:48 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.995702 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): 5.639000 59.15400 ymin,ymax (A): 2.665000 49.63000 zmin,zma (A): 14.72500 55.69500 x,y,z range (A): 53.51500 46.96500 40.97000 scale (grids/A): 1.995702 object centre (A): 32.39650 26.14750 35.21000 number of atom coordinates read : 2028 total number of charged atoms : 1902 net assigned charge : 0.9200045 assigned positive charge : 306.4247 centred at (gu) : 83.15549 88.75545 87.49989 assigned negative charge : -305.5049 centred at (gu) : 83.59225 88.83045 87.50160 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 65713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18824 grid for indexing accessible points = 1.400000 m= 24374 mr = 44809 m= 4151 mr = 17644 m= 276 mr = 2486 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15021 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) : 0.6652340 object centre at (A) : 32.39650 26.14750 35.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1598433E-03 1.3288655E-03 midg,1,midg; midg,igrid,midg 2.0801656E-02 4.8734457E-04 1,midg,midg; igrid,midg,midg -3.0787073E-02 -4.0519238E-02 gauss-seidel spectral radius is 0.9986981 estimated iterations to convergence 220 setup time was (sec) 0.9000000 now iterating at: 21:42:50 rms-change max change #iterations 4.090889 284.5071 at 10iterations 1.950392 76.56750 at 20iterations 0.9254235 38.01086 at 30iterations 0.4411534 15.72271 at 40iterations 0.2112135 7.204982 at 50iterations 0.1011477 3.603699 at 60iterations 4.8712403E-02 1.581757 at 70iterations 2.3487603E-02 0.8561478 at 80iterations 1.1607962E-02 0.3909683 at 90iterations 5.9833792E-03 0.2193375 at 100iterations 3.2857454E-03 0.1392593 at 110iterations 1.9615055E-03 7.8399658E-02 at 120iterations finished qdiffx linear iterations at : 21:42:59 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 1.9615055E-03 7.8399658E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 21:42:59 10.376u 0.432s 0:11.07 97.5% 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 Sat Oct 8 2011 at 21:42:59 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2028 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: GLM 133 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.993553 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): 5.639000 59.15400 ymin,ymax (A): 2.665000 49.63000 zmin,zma (A): 14.72500 55.69500 x,y,z range (A): 53.51500 46.96500 40.97000 scale (grids/A): 2.993553 object centre (A): 32.39650 26.14750 35.21000 number of atom coordinates read : 2028 total number of charged atoms : 1902 net assigned charge : 0.9200045 assigned positive charge : 306.4247 centred at (gu) : 79.73335 88.13318 86.24981 assigned negative charge : -305.5049 centred at (gu) : 80.38837 88.24566 86.25226 start vw surface at 0.1100000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 151340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18824 grid for indexing accessible points = 1.400000 m= 77313 mr = 108187 m= 29523 mr = 62606 m= 7567 mr = 23353 m= 1079 mr = 5441 m= 53 mr = 610 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 66660 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 15216 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) : 1.995702 object centre at (A) : 32.39650 26.14750 35.21000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2098769E-02 -3.4965514E-03 midg,1,midg; midg,igrid,midg 0.2057182 -8.3313063E-02 1,midg,midg; igrid,midg,midg -0.5854019 -0.5404812 gauss-seidel spectral radius is 0.9992695 estimated iterations to convergence 292 setup time was (sec) 1.790000 now iterating at: 21:43:02 rms-change max change #iterations 9.591193 356.6886 at 10iterations 5.702909 131.2802 at 20iterations 3.357928 77.55660 at 30iterations 1.973861 43.54200 at 40iterations 1.153323 25.00535 at 50iterations 0.6748483 13.38760 at 60iterations 0.3932449 8.219164 at 70iterations 0.2284825 4.598861 at 80iterations 0.1326540 2.619068 at 90iterations 7.7081978E-02 1.537632 at 100iterations 4.4618938E-02 0.9338531 at 110iterations 2.5910798E-02 0.5244827 at 120iterations 1.5116337E-02 0.3076859 at 130iterations 8.8582858E-03 0.1798964 at 140iterations 5.2457568E-03 0.1241570 at 150iterations 3.1923687E-03 6.9606781E-02 at 160iterations 2.0265877E-03 4.7447205E-02 at 170iterations 1.3626530E-03 3.5064697E-02 at 180iterations finished qdiffx linear iterations at : 21:43:18 total time elapsed so far: 17.75000 # loops : 180 mean,max change (kT/e) : 1.3626530E-03 3.5064697E-02 energy calculations done at 17.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.92000 DelPhi exited at 21:43:18 17.925u 0.464s 0:18.66 98.4% 0+0k 0+0io 0pf+0w