Mon Oct 10 17:03:48 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+sph.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 = amb.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 17:03:48 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5743881 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): -23.18600 26.92700 ymin,ymax (A): -63.87100 -3.530000 zmin,zma (A): -58.06300 3.916000 x,y,z range (A): 50.11300 60.34100 61.97900 scale (grids/A): 0.5743881 object centre (A): 1.870501 -33.70050 -27.07350 number of atom coordinates read : 3108 total number of charged atoms : 2955 net assigned charge : -2.499965 assigned positive charge : 464.0318 centred at (gu) : 91.30627 89.68575 91.00514 assigned negative charge : -466.5330 centred at (gu) : 91.34796 89.87509 91.07550 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6601 nv = 96 ne = 84 npr = 63406 no. pairs analyzed = 63406 no. exposed pairs = 3961 no. arc points = 27891 no. surface atoms = 1341 nbur = 1767 mkacc time = 0.1800000 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 = 1.484000 m= 251 mr = 3376 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.4200000 number of dielectric boundary points 3461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2834 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 8531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0606204E-10 -2.2680844E-09 midg,1,midg; midg,igrid,midg 3.3505070E-09 -3.8284473E-09 1,midg,midg; igrid,midg,midg 2.6080277E-10 -1.6771775E-09 gauss-seidel spectral radius is 0.9843689 estimated iterations to convergence 66 setup time was (sec) 0.7200000 now iterating at: 17:03:49 rms-change max change #iterations 9.4409212E-02 16.60102 at 10iterations 7.1708518E-03 1.014776 at 20iterations 5.6055689E-04 7.6984406E-02 at 30iterations 5.3846143E-05 9.8419189E-03 at 40iterations 7.6208480E-06 1.6746521E-03 at 50iterations finished qdiffx linear iterations at : 17:03:52 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 7.6208480E-06 1.6746521E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 17:03:54 4.277u 0.246s 0:05.66 79.6% 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 17:03:54 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.723164 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): -23.18600 26.92700 ymin,ymax (A): -63.87100 -3.530000 zmin,zma (A): -58.06300 3.916000 x,y,z range (A): 50.11300 60.34100 61.97900 scale (grids/A): 1.723164 object centre (A): 1.870501 -33.70050 -27.07350 number of atom coordinates read : 3108 total number of charged atoms : 2955 net assigned charge : -2.499965 assigned positive charge : 464.0318 centred at (gu) : 93.91788 89.05614 93.01431 assigned negative charge : -466.5330 centred at (gu) : 94.04338 89.62486 93.22614 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 73011 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27891 grid for indexing accessible points = 1.400000 m= 21674 mr = 49241 m= 2152 mr = 14518 m= 64 mr = 1052 m= 0 mr = 8 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1135 time to turn everything in is 0.6500000 number of dielectric boundary points 32082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22867 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) : 0.5743881 object centre at (A) : 1.870501 -33.70050 -27.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9943895E-04 -1.3192819E-02 midg,1,midg; midg,igrid,midg 1.9266408E-02 -3.5526283E-02 1,midg,midg; igrid,midg,midg 1.4585066E-04 -8.8020274E-03 gauss-seidel spectral radius is 0.9983867 estimated iterations to convergence 198 setup time was (sec) 1.030000 now iterating at: 17:03:55 rms-change max change #iterations 3.818745 181.9954 at 10iterations 1.674244 67.03109 at 20iterations 0.7313545 26.04512 at 30iterations 0.3194265 11.73604 at 40iterations 0.1402863 4.586876 at 50iterations 6.1458483E-02 2.061421 at 60iterations 2.6961297E-02 1.072403 at 70iterations 1.1762731E-02 0.3801672 at 80iterations 5.1836516E-03 0.1651430 at 90iterations 2.2740178E-03 7.4731827E-02 at 100iterations 1.0000326E-03 3.4782410E-02 at 110iterations 4.4090583E-04 1.4816284E-02 at 120iterations finished qdiffx linear iterations at : 17:04:03 total time elapsed so far: 8.810000 # loops : 120 mean,max change (kT/e) : 4.4090583E-04 1.4816284E-02 energy calculations done at 8.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 17:04:04 9.059u 0.179s 0:10.29 89.6% 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 17:04:04 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.584746 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): -23.18600 26.92700 ymin,ymax (A): -63.87100 -3.530000 zmin,zma (A): -58.06300 3.916000 x,y,z range (A): 50.11300 60.34100 61.97900 scale (grids/A): 2.584746 object centre (A): 1.870501 -33.70050 -27.07350 number of atom coordinates read : 3108 total number of charged atoms : 2955 net assigned charge : -2.499965 assigned positive charge : 464.0318 centred at (gu) : 95.87668 88.58387 94.52128 assigned negative charge : -466.5330 centred at (gu) : 96.06507 89.43726 94.83904 start vw surface at 0.2700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 169745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27891 grid for indexing accessible points = 1.400000 m= 75091 mr = 120547 m= 20918 mr = 58707 m= 3338 mr = 15495 m= 244 mr = 2159 m= 4 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 3950 time to turn everything in is 1.680000 number of dielectric boundary points 72317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 23627 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) : 1.723164 object centre at (A) : 1.870501 -33.70050 -27.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3155849E-02 -0.1394828 midg,1,midg; midg,igrid,midg 0.4261009 -0.3591789 1,midg,midg; igrid,midg,midg 5.9519811E-03 -0.1180713 gauss-seidel spectral radius is 0.9992048 estimated iterations to convergence 280 setup time was (sec) 2.040000 now iterating at: 17:04:06 rms-change max change #iterations 9.632163 277.7409 at 10iterations 5.515174 145.4369 at 20iterations 3.136032 70.63248 at 30iterations 1.782226 37.84089 at 40iterations 1.010751 22.04049 at 50iterations 0.5725087 12.00767 at 60iterations 0.3232425 6.264472 at 70iterations 0.1825022 3.765280 at 80iterations 0.1029936 2.073191 at 90iterations 5.8090944E-02 1.124825 at 100iterations 3.2734115E-02 0.6336212 at 110iterations 1.8452838E-02 0.3604031 at 120iterations 1.0380512E-02 0.1990070 at 130iterations 5.8592698E-03 0.1128302 at 140iterations 3.2941473E-03 6.5793037E-02 at 150iterations 1.8607168E-03 3.5830379E-02 at 160iterations 1.0511928E-03 2.1949768E-02 at 170iterations 5.9440034E-04 1.1124253E-02 at 180iterations finished qdiffx linear iterations at : 17:04:18 total time elapsed so far: 14.28000 # loops : 180 mean,max change (kT/e) : 5.9440034E-04 1.1124253E-02 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.51000 DelPhi exited at 17:04:20 14.514u 0.197s 0:16.45 89.3% 0+0k 0+0io 0pf+0w