Tue Oct 11 07:51:12 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 Tue Oct 11 2011 at 07:51:12 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: SEP 207 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.6363734 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): -13.57300 42.36900 ymin,ymax (A): -21.77400 28.18600 zmin,zma (A): -11.63500 40.18500 x,y,z range (A): 55.94200 49.96000 51.82000 scale (grids/A): 0.6363734 object centre (A): 14.39800 3.205999 14.27500 number of atom coordinates read : 2765 total number of charged atoms : 2400 net assigned charge : 10.03902 assigned positive charge : 388.8811 centred at (gu) : 90.10904 87.79024 90.93641 assigned negative charge : -378.8427 centred at (gu) : 90.08367 87.74363 91.16613 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 6759 nv = 96 ne = 84 npr = 51493 no. pairs analyzed = 51493 no. exposed pairs = 2941 no. arc points = 20634 no. surface atoms = 1005 nbur = 1760 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3825 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3900000 number of dielectric boundary points 3222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2123 ## 239 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8149 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9803786E-08 -1.3273161E-08 midg,1,midg; midg,igrid,midg 1.3622482E-08 1.1504375E-08 1,midg,midg; igrid,midg,midg 1.0630232E-08 1.6435633E-08 gauss-seidel spectral radius is 0.9871961 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 07:51:13 rms-change max change #iterations 0.1450590 22.72541 at 10iterations 1.4516674E-02 2.478291 at 20iterations 1.7493891E-03 0.2403870 at 30iterations 2.8128506E-04 4.0298462E-02 at 40iterations 5.8232868E-05 8.5411072E-03 at 50iterations finished qdiffx linear iterations at : 07:51:15 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.8232868E-05 8.5411072E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 07:51:16 3.423u 0.145s 0:04.01 88.7% 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 Tue Oct 11 2011 at 07:51:16 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: SEP 207 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.909120 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): -13.57300 42.36900 ymin,ymax (A): -21.77400 28.18600 zmin,zma (A): -11.63500 40.18500 x,y,z range (A): 55.94200 49.96000 51.82000 scale (grids/A): 1.909120 object centre (A): 14.39800 3.205999 14.27500 number of atom coordinates read : 2765 total number of charged atoms : 2400 net assigned charge : 10.03902 assigned positive charge : 388.8811 centred at (gu) : 90.32661 83.37032 92.80883 assigned negative charge : -378.8427 centred at (gu) : 90.25062 83.23074 93.49802 start vw surface at 0.2300000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 72823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20634 grid for indexing accessible points = 1.400000 m= 27107 mr = 51440 m= 4034 mr = 20504 m= 213 mr = 2541 m= 4 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 528 time to turn everything in is 0.6500000 number of dielectric boundary points 29612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18846 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) : 0.6363734 object centre at (A) : 14.39800 3.205999 14.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5846144E-02 -1.3790390E-02 midg,1,midg; midg,igrid,midg 1.2473011E-02 2.3731519E-02 1,midg,midg; igrid,midg,midg 2.3153555E-02 4.4287868E-02 gauss-seidel spectral radius is 0.9986250 estimated iterations to convergence 214 setup time was (sec) 0.9500000 now iterating at: 07:51:17 rms-change max change #iterations 4.188772 211.2398 at 10iterations 1.960583 67.36816 at 20iterations 0.9182979 29.47767 at 30iterations 0.4295422 13.71240 at 40iterations 0.2018710 6.577223 at 50iterations 9.4417065E-02 2.859581 at 60iterations 4.4269625E-02 1.449161 at 70iterations 2.0840090E-02 0.7311401 at 80iterations 9.8049110E-03 0.3121252 at 90iterations 4.6469043E-03 0.1557875 at 100iterations 2.2154299E-03 7.5344086E-02 at 110iterations 1.0733785E-03 3.6006927E-02 at 120iterations finished qdiffx linear iterations at : 07:51:24 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 1.0733785E-03 3.6006927E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 07:51:24 7.861u 0.181s 0:08.39 95.8% 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 Tue Oct 11 2011 at 07:51:24 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2765 !!! WARNING: HIQ 55 has a net charge of 0.5140 !!! WARNING: SEP 207 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.863680 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): -13.57300 42.36900 ymin,ymax (A): -21.77400 28.18600 zmin,zma (A): -11.63500 40.18500 x,y,z range (A): 55.94200 49.96000 51.82000 scale (grids/A): 2.863680 object centre (A): 14.39800 3.205999 14.27500 number of atom coordinates read : 2765 total number of charged atoms : 2400 net assigned charge : 10.03902 assigned positive charge : 388.8811 centred at (gu) : 90.48965 80.05525 94.21314 assigned negative charge : -378.8427 centred at (gu) : 90.37583 79.84604 95.24696 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20634 grid for indexing accessible points = 1.400000 m= 87684 mr = 124161 m= 31793 mr = 73123 m= 7332 mr = 25891 m= 997 mr = 5500 m= 53 mr = 729 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 1941 time to turn everything in is 1.410000 number of dielectric boundary points 66885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19197 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) : 1.909120 object centre at (A) : 14.39800 3.205999 14.27500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7223827 -0.2266849 midg,1,midg; midg,igrid,midg 0.1075731 0.2417867 1,midg,midg; igrid,midg,midg 0.1709741 0.3175471 gauss-seidel spectral radius is 0.9992453 estimated iterations to convergence 287 setup time was (sec) 1.720000 now iterating at: 07:51:26 rms-change max change #iterations 9.735055 328.5923 at 10iterations 5.634562 147.9982 at 20iterations 3.247765 64.57339 at 30iterations 1.868139 36.13428 at 40iterations 1.070742 19.62142 at 50iterations 0.6149161 11.67095 at 60iterations 0.3518483 6.663145 at 70iterations 0.2019138 3.627045 at 80iterations 0.1157633 2.213570 at 90iterations 6.6236787E-02 1.161373 at 100iterations 3.7970029E-02 0.6910124 at 110iterations 2.1888647E-02 0.3972740 at 120iterations 1.2657374E-02 0.2306709 at 130iterations 7.3966249E-03 0.1360397 at 140iterations 4.3741376E-03 8.6112976E-02 at 150iterations 2.6551690E-03 5.4147720E-02 at 160iterations 1.6610667E-03 3.1166077E-02 at 170iterations 1.0863945E-03 2.1274567E-02 at 180iterations finished qdiffx linear iterations at : 07:51:37 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 1.0863945E-03 2.1274567E-02 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 07:51:37 12.258u 0.231s 0:12.96 96.2% 0+0k 0+0io 0pf+0w