Mon Oct 10 14:01:03 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 14:01:04 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6395975 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): -11.86200 43.68800 ymin,ymax (A): -22.52500 22.34200 zmin,zma (A): -6.900000 48.76000 x,y,z range (A): 55.55000 44.86700 55.66000 scale (grids/A): 0.6395975 object centre (A): 15.91300 -9.1500282E-02 20.93000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0425 centred at (gu) : 88.74680 89.70011 91.13702 assigned negative charge : -454.0433 centred at (gu) : 88.72283 89.60497 91.05624 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8178 nv = 96 ne = 84 npr = 63788 no. pairs analyzed = 63788 no. exposed pairs = 3452 no. arc points = 24061 no. surface atoms = 1166 nbur = 1865 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 442 mr = 4796 m= 4 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2237 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9962 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6008551E-09 1.3787366E-08 midg,1,midg; midg,igrid,midg -1.3861210E-08 1.1836104E-08 1,midg,midg; igrid,midg,midg -4.3130277E-09 2.4221072E-09 gauss-seidel spectral radius is 0.9873650 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 14:01:05 rms-change max change #iterations 0.1566731 23.71372 at 10iterations 1.5819332E-02 2.412863 at 20iterations 1.7330522E-03 0.2086906 at 30iterations 2.3041756E-04 2.7332306E-02 at 40iterations 4.1559659E-05 5.9356689E-03 at 50iterations finished qdiffx linear iterations at : 14:01:09 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 4.1559659E-05 5.9356689E-03 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 14:01:09 4.747u 0.410s 0:05.61 91.8% 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 14:01:09 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.918792 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): -11.86200 43.68800 ymin,ymax (A): -22.52500 22.34200 zmin,zma (A): -6.900000 48.76000 x,y,z range (A): 55.55000 44.86700 55.66000 scale (grids/A): 1.918792 object centre (A): 15.91300 -9.1500282E-02 20.93000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0425 centred at (gu) : 86.23973 89.09988 93.41059 assigned negative charge : -454.0433 centred at (gu) : 86.16824 88.81448 93.16856 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24061 grid for indexing accessible points = 1.400000 m= 32545 mr = 64859 m= 4991 mr = 24416 m= 268 mr = 3018 m= 7 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 248 time to turn everything in is 0.6900000 number of dielectric boundary points 34675 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 22719 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) : 0.6395975 object centre at (A) : 15.91300 -9.1500282E-02 20.93000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4388744E-02 1.9149622E-02 midg,1,midg; midg,igrid,midg -3.3201932E-03 1.5366104E-02 1,midg,midg; igrid,midg,midg -3.2362878E-02 1.6113931E-02 gauss-seidel spectral radius is 0.9986873 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 14:01:11 rms-change max change #iterations 4.761159 177.3326 at 10iterations 2.271002 68.73280 at 20iterations 1.079663 31.41963 at 30iterations 0.5142949 14.67355 at 40iterations 0.2448790 7.084690 at 50iterations 0.1166275 3.303894 at 60iterations 5.5619232E-02 1.854107 at 70iterations 2.6425583E-02 0.7170295 at 80iterations 1.2663630E-02 0.4119182 at 90iterations 6.0162046E-03 0.1862701 at 100iterations 2.8823123E-03 8.4722519E-02 at 110iterations 1.3771346E-03 4.1023254E-02 at 120iterations finished qdiffx linear iterations at : 14:01:21 total time elapsed so far: 10.90000 # loops : 120 mean,max change (kT/e) : 1.3771346E-03 4.1023254E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.06000 DelPhi exited at 14:01:22 11.062u 0.459s 0:12.42 92.6% 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 14:01:22 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3031 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.878189 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): -11.86200 43.68800 ymin,ymax (A): -22.52500 22.34200 zmin,zma (A): -6.900000 48.76000 x,y,z range (A): 55.55000 44.86700 55.66000 scale (grids/A): 2.878189 object centre (A): 15.91300 -9.1500282E-02 20.93000 number of atom coordinates read : 3031 total number of charged atoms : 2884 net assigned charge : 7.1674585E-06 assigned positive charge : 454.0425 centred at (gu) : 84.35960 88.64979 95.11562 assigned negative charge : -454.0433 centred at (gu) : 84.25232 88.22179 94.75258 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 207099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24061 grid for indexing accessible points = 1.400000 m= 106693 mr = 156683 m= 37663 mr = 88984 m= 8866 mr = 30355 m= 1274 mr = 6499 m= 50 mr = 811 m= 0 mr = 2 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 858 time to turn everything in is 1.900000 number of dielectric boundary points 78311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 23068 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) : 1.918792 object centre at (A) : 15.91300 -9.1500282E-02 20.93000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1046517E-02 0.2769981 midg,1,midg; midg,igrid,midg -1.8767821E-02 0.1697835 1,midg,midg; igrid,midg,midg -0.4261147 0.2728320 gauss-seidel spectral radius is 0.9992748 estimated iterations to convergence 293 setup time was (sec) 2.230000 now iterating at: 14:01:25 rms-change max change #iterations 11.00163 430.3275 at 10iterations 6.477622 140.8701 at 20iterations 3.775638 84.65766 at 30iterations 2.200478 46.37225 at 40iterations 1.279173 22.45449 at 50iterations 0.7441726 14.61435 at 60iterations 0.4314650 8.060733 at 70iterations 0.2506399 4.416658 at 80iterations 0.1452514 2.523078 at 90iterations 8.4151432E-02 1.567863 at 100iterations 4.8815556E-02 0.8339729 at 110iterations 2.8278235E-02 0.4772526 at 120iterations 1.6391108E-02 0.2544079 at 130iterations 9.5092580E-03 0.1584587 at 140iterations 5.5119875E-03 9.1514587E-02 at 150iterations 3.2084568E-03 5.2326202E-02 at 160iterations 1.8785823E-03 3.2564163E-02 at 170iterations 1.1042103E-03 1.8795490E-02 at 180iterations finished qdiffx linear iterations at : 14:01:42 total time elapsed so far: 19.27000 # loops : 180 mean,max change (kT/e) : 1.1042103E-03 1.8795490E-02 energy calculations done at 19.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.43000 DelPhi exited at 14:01:42 19.439u 0.463s 0:20.31 97.9% 0+0k 0+0io 0pf+0w