Sat Oct 8 19:08:38 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 8 2011 at 19:08:38 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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: 0.6245504 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): -31.98900 17.46400 ymin,ymax (A): -25.48500 21.91500 zmin,zma (A): -12.56000 44.44100 x,y,z range (A): 49.45300 47.40000 57.00100 scale (grids/A): 0.6245504 object centre (A): -7.262500 -1.785000 15.94050 number of atom coordinates read : 2602 total number of charged atoms : 2458 net assigned charge : 4.720007 assigned positive charge : 394.6520 centred at (gu) : 88.53854 89.21988 89.92696 assigned negative charge : -389.9326 centred at (gu) : 88.42406 89.26227 89.81306 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6758 nv = 96 ne = 84 npr = 53507 no. pairs analyzed = 53507 no. exposed pairs = 3032 no. arc points = 21658 no. surface atoms = 1029 nbur = 1573 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3822 m= 0 mr = 46 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.1900000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8209 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3483093E-09 1.2814992E-08 midg,1,midg; midg,igrid,midg 9.1072021E-09 1.0851754E-09 1,midg,midg; igrid,midg,midg -6.1108487E-09 9.5120596E-09 gauss-seidel spectral radius is 0.9867208 estimated iterations to convergence 71 setup time was (sec) 0.3900000 now iterating at: 19:08:38 rms-change max change #iterations 0.1341361 19.05851 at 10iterations 1.2669098E-02 2.295174 at 20iterations 1.1865578E-03 0.1659412 at 30iterations 1.1341732E-04 1.6309738E-02 at 40iterations 1.0635842E-05 1.6899109E-03 at 50iterations finished qdiffx linear iterations at : 19:08:41 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.0635842E-05 1.6899109E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 19:08:42 3.499u 0.194s 0:03.96 92.9% 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 Sat Oct 8 2011 at 19:08:42 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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: 1.873651 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): -31.98900 17.46400 ymin,ymax (A): -25.48500 21.91500 zmin,zma (A): -12.56000 44.44100 x,y,z range (A): 49.45300 47.40000 57.00100 scale (grids/A): 1.873651 object centre (A): -7.262500 -1.785000 15.94050 number of atom coordinates read : 2602 total number of charged atoms : 2458 net assigned charge : 4.720007 assigned positive charge : 394.6520 centred at (gu) : 85.61534 87.65916 89.78054 assigned negative charge : -389.9326 centred at (gu) : 85.27214 87.78664 89.43884 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21658 grid for indexing accessible points = 1.400000 m= 26733 mr = 51192 m= 4250 mr = 20264 m= 217 mr = 2738 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3031 time to turn everything in is 0.3700000 number of dielectric boundary points 29963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 19309 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) : 0.6245504 object centre at (A) : -7.262500 -1.785000 15.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7659202E-02 3.0305993E-02 midg,1,midg; midg,igrid,midg 1.6220530E-02 2.2594132E-03 1,midg,midg; igrid,midg,midg -6.0034911E-03 3.9130133E-02 gauss-seidel spectral radius is 0.9985893 estimated iterations to convergence 211 setup time was (sec) 0.6000000 now iterating at: 19:08:43 rms-change max change #iterations 4.073021 191.6790 at 10iterations 1.884532 72.37061 at 20iterations 0.8721393 27.75066 at 30iterations 0.4029259 13.15005 at 40iterations 0.1868311 5.963402 at 50iterations 8.6588643E-02 3.096088 at 60iterations 3.9854873E-02 1.368011 at 70iterations 1.8504303E-02 0.5832710 at 80iterations 8.5570281E-03 0.2643747 at 90iterations 3.9638621E-03 0.1256409 at 100iterations 1.8335023E-03 5.5735588E-02 at 110iterations 8.4950303E-04 3.0538559E-02 at 120iterations finished qdiffx linear iterations at : 19:08:50 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 8.4950303E-04 3.0538559E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 19:08:51 8.083u 0.212s 0:08.57 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 8 2011 at 19:08:51 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2602 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 667 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: 2.810477 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): -31.98900 17.46400 ymin,ymax (A): -25.48500 21.91500 zmin,zma (A): -12.56000 44.44100 x,y,z range (A): 49.45300 47.40000 57.00100 scale (grids/A): 2.810477 object centre (A): -7.262500 -1.785000 15.94050 number of atom coordinates read : 2602 total number of charged atoms : 2458 net assigned charge : 4.720007 assigned positive charge : 394.6520 centred at (gu) : 83.42275 86.48859 89.67076 assigned negative charge : -389.9326 centred at (gu) : 82.90814 86.67987 89.15826 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21658 grid for indexing accessible points = 1.400000 m= 86669 mr = 123709 m= 31643 mr = 71948 m= 7723 mr = 25973 m= 1003 mr = 5847 m= 37 mr = 660 m= 0 mr = 8 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 9879 time to turn everything in is 0.9400000 number of dielectric boundary points 67589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 19663 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) : 1.873651 object centre at (A) : -7.262500 -1.785000 15.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4882179E-02 0.3890871 midg,1,midg; midg,igrid,midg 0.2127867 2.6111627E-02 1,midg,midg; igrid,midg,midg -4.9682133E-02 0.4722586 gauss-seidel spectral radius is 0.9992403 estimated iterations to convergence 286 setup time was (sec) 1.190000 now iterating at: 19:08:52 rms-change max change #iterations 9.631076 319.4190 at 10iterations 5.565672 128.3853 at 20iterations 3.193095 65.42204 at 30iterations 1.827060 38.73475 at 40iterations 1.047883 19.85794 at 50iterations 0.5978324 11.99593 at 60iterations 0.3409889 6.534303 at 70iterations 0.1955531 3.504807 at 80iterations 0.1113291 2.193518 at 90iterations 6.3403085E-02 1.279928 at 100iterations 3.6278099E-02 0.6319113 at 110iterations 2.0634694E-02 0.4331779 at 120iterations 1.1789707E-02 0.2104912 at 130iterations 6.7248647E-03 0.1210151 at 140iterations 3.8248820E-03 7.1091652E-02 at 150iterations 2.1818771E-03 4.2915344E-02 at 160iterations 1.2449711E-03 2.3798943E-02 at 170iterations 7.1153668E-04 1.6759157E-02 at 180iterations finished qdiffx linear iterations at : 19:09:04 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 7.1153668E-04 1.6759157E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 19:09:04 13.219u 0.243s 0:13.73 97.9% 0+0k 0+0io 0pf+0w