Sat Oct 15 14:59:02 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 15 2011 at 14:59:02 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! WARNING: HIR 235 has a net charge of 0.5140 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: 0.6218776 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): -11.43500 45.50000 ymin,ymax (A): 30.28800 83.07000 zmin,zma (A): -12.67800 44.56800 x,y,z range (A): 56.93500 52.78200 57.24599 scale (grids/A): 0.6218776 object centre (A): 17.03250 56.67900 15.94500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 1.4012337E-02 assigned positive charge : 386.0738 centred at (gu) : 89.32526 90.88473 90.59502 assigned negative charge : -386.0609 centred at (gu) : 89.36147 90.95594 90.57639 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6761 nv = 96 ne = 84 npr = 52198 no. pairs analyzed = 52198 no. exposed pairs = 3584 no. arc points = 25509 no. surface atoms = 1190 nbur = 1410 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3331 m= 0 mr = 45 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8203 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1095926E-09 1.5226793E-09 midg,1,midg; midg,igrid,midg 4.0742063E-09 -6.0668324E-09 1,midg,midg; igrid,midg,midg 2.9668827E-09 -2.1499047E-09 gauss-seidel spectral radius is 0.9866212 estimated iterations to convergence 71 setup time was (sec) 0.4500000 now iterating at: 14:59:03 rms-change max change #iterations 0.1261138 17.22326 at 10iterations 1.1543784E-02 1.834484 at 20iterations 1.0688525E-03 0.1760521 at 30iterations 1.0303028E-04 1.6365051E-02 at 40iterations 1.0506330E-05 1.7008781E-03 at 50iterations finished qdiffx linear iterations at : 14:59:07 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.0506330E-05 1.7008781E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 14:59:07 4.311u 0.304s 0:04.88 94.4% 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 15 2011 at 14:59:07 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! WARNING: HIR 235 has a net charge of 0.5140 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: 1.865633 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): -11.43500 45.50000 ymin,ymax (A): 30.28800 83.07000 zmin,zma (A): -12.67800 44.56800 x,y,z range (A): 56.93500 52.78200 57.24599 scale (grids/A): 1.865633 object centre (A): 17.03250 56.67900 15.94500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 1.4012337E-02 assigned positive charge : 386.0738 centred at (gu) : 87.97504 92.65363 91.78444 assigned negative charge : -386.0609 centred at (gu) : 88.08440 92.86792 91.72914 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25509 grid for indexing accessible points = 1.400000 m= 24461 mr = 47162 m= 3645 mr = 16857 m= 169 mr = 2019 m= 0 mr = 34 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34682 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 200 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 19373 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) : 0.6218776 object centre at (A) : 17.03250 56.67900 15.94500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3796950E-03 -2.3475530E-02 midg,1,midg; midg,igrid,midg 1.6254820E-02 -1.4095410E-02 1,midg,midg; igrid,midg,midg 2.3484036E-02 1.9262608E-05 gauss-seidel spectral radius is 0.9985988 estimated iterations to convergence 212 setup time was (sec) 0.7000000 now iterating at: 14:59:08 rms-change max change #iterations 4.081478 174.5070 at 10iterations 1.879041 65.50230 at 20iterations 0.8714265 28.54891 at 30iterations 0.4029541 13.44077 at 40iterations 0.1869522 6.450338 at 50iterations 8.6285323E-02 2.952253 at 60iterations 4.0095214E-02 1.216591 at 70iterations 1.8572222E-02 0.6070170 at 80iterations 8.5600922E-03 0.3418579 at 90iterations 3.9720070E-03 0.1247730 at 100iterations 1.8447291E-03 6.0889244E-02 at 110iterations 8.5509248E-04 2.9319763E-02 at 120iterations finished qdiffx linear iterations at : 14:59:18 total time elapsed so far: 10.16000 # loops : 120 mean,max change (kT/e) : 8.5509248E-04 2.9319763E-02 energy calculations done at 10.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.30000 DelPhi exited at 14:59:18 10.300u 0.344s 0:11.00 96.7% 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 15 2011 at 14:59:18 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2600 !!! WARNING: HIR 235 has a net charge of 0.5140 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: 2.798449 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): -11.43500 45.50000 ymin,ymax (A): 30.28800 83.07000 zmin,zma (A): -12.67800 44.56800 x,y,z range (A): 56.93500 52.78200 57.24599 scale (grids/A): 2.798449 object centre (A): 17.03250 56.67900 15.94500 number of atom coordinates read : 2600 total number of charged atoms : 2463 net assigned charge : 1.4012337E-02 assigned positive charge : 386.0738 centred at (gu) : 86.96236 93.98039 92.67643 assigned negative charge : -386.0609 centred at (gu) : 87.12661 94.30193 92.59376 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 167474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25509 grid for indexing accessible points = 1.400000 m= 78922 mr = 115261 m= 27699 mr = 61820 m= 6168 mr = 21108 m= 706 mr = 4232 m= 18 mr = 380 m= 0 mr = 8 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 78178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 19702 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) : 1.865633 object centre at (A) : 17.03250 56.67900 15.94500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6825737E-02 -0.2494059 midg,1,midg; midg,igrid,midg 0.2289351 -2.6280321E-02 1,midg,midg; igrid,midg,midg 0.2888595 -1.7704910E-02 gauss-seidel spectral radius is 0.9992598 estimated iterations to convergence 290 setup time was (sec) 1.390000 now iterating at: 14:59:20 rms-change max change #iterations 9.810232 354.0220 at 10iterations 5.766965 160.7343 at 20iterations 3.357776 76.22120 at 30iterations 1.951580 43.91827 at 40iterations 1.131195 24.91144 at 50iterations 0.6516048 13.53789 at 60iterations 0.3758447 7.903097 at 70iterations 0.2166739 4.224606 at 80iterations 0.1246736 2.392275 at 90iterations 7.1772642E-02 1.303360 at 100iterations 4.1237384E-02 0.7930565 at 110iterations 2.3640132E-02 0.4547653 at 120iterations 1.3587561E-02 0.2789383 at 130iterations 7.7997679E-03 0.1515388 at 140iterations 4.4854158E-03 9.3236208E-02 at 150iterations 2.5760981E-03 4.4706345E-02 at 160iterations 1.4771475E-03 2.6707649E-02 at 170iterations 8.5112237E-04 1.6500533E-02 at 180iterations finished qdiffx linear iterations at : 14:59:36 total time elapsed so far: 17.05000 # loops : 180 mean,max change (kT/e) : 8.5112237E-04 1.6500533E-02 energy calculations done at 17.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.18000 DelPhi exited at 14:59:36 17.184u 0.367s 0:17.96 97.6% 0+0k 0+0io 0pf+0w