Tue Nov 22 14:15:23 PST 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 Tue Nov 22 2011 at 14:15:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6539310 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): -5.126000 34.81500 ymin,ymax (A): -3.454000 49.30800 zmin,zma (A): -7.892000 46.54800 x,y,z range (A): 39.94100 52.76200 54.44000 scale (grids/A): 0.6539310 object centre (A): 14.84450 22.92700 19.32800 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 286.9601 centred at (gu) : 89.34027 92.22731 90.12177 assigned negative charge : -281.9603 centred at (gu) : 89.26299 92.33849 90.17941 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5793 nv = 96 ne = 84 npr = 39710 no. pairs analyzed = 39710 no. exposed pairs = 2582 no. arc points = 18245 no. surface atoms = 876 nbur = 1080 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 310 mr = 3129 m= 3 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2941 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1867 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6735 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7684810E-08 4.1552588E-09 midg,1,midg; midg,igrid,midg 1.5516436E-08 -4.6729713E-09 1,midg,midg; igrid,midg,midg 1.7830306E-09 1.7881680E-08 gauss-seidel spectral radius is 0.9878277 estimated iterations to convergence 74 setup time was (sec) 0.3900000 now iterating at: 14:15:32 rms-change max change #iterations 0.1351240 20.77975 at 10iterations 1.3578779E-02 2.068021 at 20iterations 1.4091202E-03 0.2493243 at 30iterations 1.4705784E-04 2.3180008E-02 at 40iterations 1.5106829E-05 2.3040771E-03 at 50iterations finished qdiffx linear iterations at : 14:15:42 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 1.5106829E-05 2.3040771E-03 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 14:15:43 3.847u 0.210s 0:15.69 25.8% 0+0k 0+0io 3pf+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 Tue Nov 22 2011 at 14:15:45 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.961793 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): -5.126000 34.81500 ymin,ymax (A): -3.454000 49.30800 zmin,zma (A): -7.892000 46.54800 x,y,z range (A): 39.94100 52.76200 54.44000 scale (grids/A): 1.961793 object centre (A): 14.84450 22.92700 19.32800 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 286.9601 centred at (gu) : 88.02100 96.68217 90.36536 assigned negative charge : -281.9603 centred at (gu) : 87.78927 97.01571 90.53854 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 62053 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 22747 mr = 42058 m= 3438 mr = 17113 m= 194 mr = 2181 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 450 time to turn everything in is 0.3300000 number of dielectric boundary points 27024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14405 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) : 0.6539310 object centre at (A) : 14.84450 22.92700 19.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1641713E-02 3.2853667E-02 midg,1,midg; midg,igrid,midg 4.1999806E-02 1.5017705E-03 1,midg,midg; igrid,midg,midg 6.9164867E-03 1.1427717E-02 gauss-seidel spectral radius is 0.9986394 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 14:15:50 rms-change max change #iterations 3.719938 161.2855 at 10iterations 1.745201 68.89005 at 20iterations 0.8142843 30.04617 at 30iterations 0.3825218 14.18468 at 40iterations 0.1789254 6.712631 at 50iterations 8.3643004E-02 2.765182 at 60iterations 3.9231166E-02 1.310322 at 70iterations 1.8400857E-02 0.6849594 at 80iterations 8.6016022E-03 0.2794329 at 90iterations 4.0275007E-03 0.1405803 at 100iterations 1.8794277E-03 6.5475464E-02 at 110iterations 8.8278722E-04 3.2373190E-02 at 120iterations finished qdiffx linear iterations at : 14:16:14 total time elapsed so far: 8.670000 # loops : 120 mean,max change (kT/e) : 8.8278722E-04 3.2373190E-02 energy calculations done at 8.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.800000 DelPhi exited at 14:16:15 8.801u 0.252s 0:30.99 29.2% 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 Tue Nov 22 2011 at 14:16:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1956 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.942689 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): -5.126000 34.81500 ymin,ymax (A): -3.454000 49.30800 zmin,zma (A): -7.892000 46.54800 x,y,z range (A): 39.94100 52.76200 54.44000 scale (grids/A): 2.942689 object centre (A): 14.84450 22.92700 19.32800 number of atom coordinates read : 1956 total number of charged atoms : 1824 net assigned charge : 5.000011 assigned positive charge : 286.9601 centred at (gu) : 87.03154 100.0232 90.54802 assigned negative charge : -281.9603 centred at (gu) : 86.68401 100.5237 90.80790 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 143094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18245 grid for indexing accessible points = 1.400000 m= 73001 mr = 101895 m= 27058 mr = 60095 m= 6286 mr = 22115 m= 842 mr = 4766 m= 41 mr = 533 m= 0 mr = 18 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 1533 time to turn everything in is 0.8600000 number of dielectric boundary points 60900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14592 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) : 1.961793 object centre at (A) : 14.84450 22.92700 19.32800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3203323E-03 0.7683513 midg,1,midg; midg,igrid,midg 0.4450957 -5.0957687E-02 1,midg,midg; igrid,midg,midg 0.1092097 7.9069413E-02 gauss-seidel spectral radius is 0.9992523 estimated iterations to convergence 289 setup time was (sec) 1.140000 now iterating at: 14:16:24 rms-change max change #iterations 8.854108 383.3427 at 10iterations 5.176612 152.3777 at 20iterations 3.003335 103.4281 at 30iterations 1.737954 41.51046 at 40iterations 1.002177 20.81923 at 50iterations 0.5760958 13.86807 at 60iterations 0.3311247 7.406250 at 70iterations 0.1900214 3.870693 at 80iterations 0.1090144 2.196947 at 90iterations 6.2489744E-02 1.235868 at 100iterations 3.5848599E-02 0.7395191 at 110iterations 2.0515651E-02 0.4014721 at 120iterations 1.1752256E-02 0.2169228 at 130iterations 6.7240070E-03 0.1345074 at 140iterations 3.8485208E-03 7.9307586E-02 at 150iterations 2.2004463E-03 4.4913650E-02 at 160iterations 1.2563922E-03 2.8453290E-02 at 170iterations 7.2092732E-04 1.4470577E-02 at 180iterations finished qdiffx linear iterations at : 14:17:04 total time elapsed so far: 14.35000 # loops : 180 mean,max change (kT/e) : 7.2092732E-04 1.4470577E-02 energy calculations done at 14.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.49000 DelPhi exited at 14:17:05 14.494u 0.281s 0:48.39 30.5% 0+0k 0+0io 0pf+0w