Mon Oct 10 14:02:21 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 14:02:22 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 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: 0.6217037 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): -31.97100 17.62300 ymin,ymax (A): -24.14800 23.04800 zmin,zma (A): -12.60500 44.65700 x,y,z range (A): 49.59400 47.19600 57.26200 scale (grids/A): 0.6217037 object centre (A): -7.174000 -0.5499992 16.02600 number of atom coordinates read : 2559 total number of charged atoms : 2442 net assigned charge : 3.500008 assigned positive charge : 389.4131 centred at (gu) : 88.42491 89.36790 89.97884 assigned negative charge : -385.9136 centred at (gu) : 88.33022 89.41188 89.86423 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6614 nv = 96 ne = 84 npr = 52477 no. pairs analyzed = 52477 no. exposed pairs = 3051 no. arc points = 21630 no. surface atoms = 1027 nbur = 1532 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3668 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2000000 number of dielectric boundary points 3199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2192 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9954907E-09 1.0845651E-08 midg,1,midg; midg,igrid,midg 6.9995085E-09 2.3508782E-11 1,midg,midg; igrid,midg,midg -5.1663762E-09 6.7730146E-09 gauss-seidel spectral radius is 0.9865959 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 14:02:22 rms-change max change #iterations 0.1279542 20.96289 at 10iterations 1.1938723E-02 1.740135 at 20iterations 1.1281408E-03 0.1594667 at 30iterations 1.1314598E-04 1.6455650E-02 at 40iterations 1.2827356E-05 2.2554398E-03 at 50iterations finished qdiffx linear iterations at : 14:02:25 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.2827356E-05 2.2554398E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 14:02:26 3.412u 0.179s 0:04.31 83.0% 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 14:02:26 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 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: 1.865111 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): -31.97100 17.62300 ymin,ymax (A): -24.14800 23.04800 zmin,zma (A): -12.60500 44.65700 x,y,z range (A): 49.59400 47.19600 57.26200 scale (grids/A): 1.865111 object centre (A): -7.174000 -0.5499992 16.02600 number of atom coordinates read : 2559 total number of charged atoms : 2442 net assigned charge : 3.500008 assigned positive charge : 389.4131 centred at (gu) : 85.27415 88.10341 89.93615 assigned negative charge : -385.9136 centred at (gu) : 84.99018 88.23537 89.59254 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21630 grid for indexing accessible points = 1.400000 m= 25386 mr = 49840 m= 3731 mr = 18897 m= 181 mr = 2332 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2744 time to turn everything in is 0.3400000 number of dielectric boundary points 29352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19160 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) : 0.6217037 object centre at (A) : -7.174000 -0.5499992 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0150332E-02 2.8760210E-02 midg,1,midg; midg,igrid,midg 1.3108967E-02 1.4926733E-03 1,midg,midg; igrid,midg,midg -4.6763537E-03 3.1855319E-02 gauss-seidel spectral radius is 0.9985728 estimated iterations to convergence 210 setup time was (sec) 0.5700000 now iterating at: 14:02:27 rms-change max change #iterations 4.016591 187.2480 at 10iterations 1.845460 65.12653 at 20iterations 0.8488278 29.68845 at 30iterations 0.3907721 12.99337 at 40iterations 0.1804505 5.695263 at 50iterations 8.3037287E-02 2.948517 at 60iterations 3.8302153E-02 1.301666 at 70iterations 1.7602397E-02 0.6156387 at 80iterations 8.1135891E-03 0.2692928 at 90iterations 3.7443039E-03 0.1223736 at 100iterations 1.7278832E-03 6.3949585E-02 at 110iterations 8.0011226E-04 2.8623104E-02 at 120iterations finished qdiffx linear iterations at : 14:02:34 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 8.0011226E-04 2.8623104E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 14:02:34 7.891u 0.215s 0:08.44 95.9% 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 14:02:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 701 has a net charge of 1.4000 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: 2.797667 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): -31.97100 17.62300 ymin,ymax (A): -24.14800 23.04800 zmin,zma (A): -12.60500 44.65700 x,y,z range (A): 49.59400 47.19600 57.26200 scale (grids/A): 2.797667 object centre (A): -7.174000 -0.5499992 16.02600 number of atom coordinates read : 2559 total number of charged atoms : 2442 net assigned charge : 3.500008 assigned positive charge : 389.4131 centred at (gu) : 82.91135 87.15511 89.90410 assigned negative charge : -385.9136 centred at (gu) : 82.48521 87.35303 89.38870 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 164592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21630 grid for indexing accessible points = 1.400000 m= 83363 mr = 120390 m= 29050 mr = 68802 m= 6631 mr = 23476 m= 802 mr = 4958 m= 25 mr = 517 m= 0 mr = 4 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 9548 time to turn everything in is 0.9000000 number of dielectric boundary points 66316 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19534 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) : 1.865111 object centre at (A) : -7.174000 -0.5499992 16.02600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1552900 0.3942922 midg,1,midg; midg,igrid,midg 0.1726239 1.8692380E-02 1,midg,midg; igrid,midg,midg -2.5794411E-02 0.4023276 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 1.130000 now iterating at: 14:02:36 rms-change max change #iterations 9.486339 376.4767 at 10iterations 5.467316 117.6500 at 20iterations 3.129266 57.09668 at 30iterations 1.789568 34.26421 at 40iterations 1.021173 20.18744 at 50iterations 0.5840269 10.34768 at 60iterations 0.3334496 6.540884 at 70iterations 0.1899281 3.737185 at 80iterations 0.1079951 2.147334 at 90iterations 6.1635718E-02 1.203783 at 100iterations 3.5103448E-02 0.6551323 at 110iterations 1.9982468E-02 0.3491287 at 120iterations 1.1400933E-02 0.2094421 at 130iterations 6.4961612E-03 0.1256752 at 140iterations 3.7084159E-03 6.9665432E-02 at 150iterations 2.1147705E-03 4.1868210E-02 at 160iterations 1.2115525E-03 2.2800446E-02 at 170iterations 6.9904677E-04 1.3758659E-02 at 180iterations finished qdiffx linear iterations at : 14:02:47 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 6.9904677E-04 1.3758659E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 14:02:48 12.574u 0.206s 0:13.24 96.4% 0+0k 0+0io 0pf+0w