Mon Oct 10 14:07:41 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 14:07:41 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 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: 0.6303563 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): -16.76400 39.71200 ymin,ymax (A): -41.02300 -3.7999988E-02 zmin,zma (A): -26.47600 23.78900 x,y,z range (A): 56.47600 40.98500 50.26500 scale (grids/A): 0.6303563 object centre (A): 11.47400 -20.53050 -1.343500 number of atom coordinates read : 2735 total number of charged atoms : 2370 net assigned charge : 11.00001 assigned positive charge : 368.9817 centred at (gu) : 90.02551 89.54253 90.15757 assigned negative charge : -357.9827 centred at (gu) : 90.08272 89.45542 90.10125 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6893 nv = 96 ne = 84 npr = 48776 no. pairs analyzed = 48776 no. exposed pairs = 3420 no. arc points = 23717 no. surface atoms = 1147 nbur = 1588 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3642 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2264 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8146 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2232456E-09 1.7314196E-08 midg,1,midg; midg,igrid,midg 5.3259424E-09 1.7453001E-08 1,midg,midg; igrid,midg,midg 1.6724528E-08 7.4203350E-09 gauss-seidel spectral radius is 0.9869634 estimated iterations to convergence 72 setup time was (sec) 0.3900000 now iterating at: 14:07:41 rms-change max change #iterations 0.1260219 19.14589 at 10iterations 1.2367544E-02 1.882282 at 20iterations 1.4529924E-03 0.2233124 at 30iterations 3.9962790E-04 6.0939789E-02 at 40iterations 1.7280142E-04 2.7958870E-02 at 50iterations finished qdiffx linear iterations at : 14:07:44 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.7280142E-04 2.7958870E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:07:45 3.370u 0.156s 0:04.21 83.6% 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 14:07:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 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: 1.891069 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): -16.76400 39.71200 ymin,ymax (A): -41.02300 -3.7999988E-02 zmin,zma (A): -26.47600 23.78900 x,y,z range (A): 56.47600 40.98500 50.26500 scale (grids/A): 1.891069 object centre (A): 11.47400 -20.53050 -1.343500 number of atom coordinates read : 2735 total number of charged atoms : 2370 net assigned charge : 11.00001 assigned positive charge : 368.9817 centred at (gu) : 90.07597 88.62690 90.47197 assigned negative charge : -357.9827 centred at (gu) : 90.24816 88.36590 90.30358 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23717 grid for indexing accessible points = 1.400000 m= 26680 mr = 50499 m= 4242 mr = 19031 m= 257 mr = 2429 m= 4 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 33261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18475 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) : 0.6303563 object centre at (A) : 11.47400 -20.53050 -1.343500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3362193E-02 4.2729046E-02 midg,1,midg; midg,igrid,midg 1.7549697E-02 1.4523713E-02 1,midg,midg; igrid,midg,midg 2.0261256E-02 4.2235322E-02 gauss-seidel spectral radius is 0.9986179 estimated iterations to convergence 213 setup time was (sec) 0.5800000 now iterating at: 14:07:46 rms-change max change #iterations 4.024568 186.4673 at 10iterations 1.884233 69.44543 at 20iterations 0.8854386 29.05126 at 30iterations 0.4137852 14.01882 at 40iterations 0.1940234 5.911574 at 50iterations 9.0416908E-02 2.948659 at 60iterations 4.2484496E-02 1.400375 at 70iterations 1.9894697E-02 0.6492128 at 80iterations 9.3128504E-03 0.3120360 at 90iterations 4.4442983E-03 0.1436377 at 100iterations 2.1635243E-03 7.7882200E-02 at 110iterations 1.1085136E-03 3.7410736E-02 at 120iterations finished qdiffx linear iterations at : 14:07:53 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.1085136E-03 3.7410736E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 14:07:54 7.738u 0.180s 0:09.00 87.8% 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 14:07:54 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2735 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: 2.836603 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): -16.76400 39.71200 ymin,ymax (A): -41.02300 -3.7999988E-02 zmin,zma (A): -26.47600 23.78900 x,y,z range (A): 56.47600 40.98500 50.26500 scale (grids/A): 2.836603 object centre (A): 11.47400 -20.53050 -1.343500 number of atom coordinates read : 2735 total number of charged atoms : 2370 net assigned charge : 11.00001 assigned positive charge : 368.9817 centred at (gu) : 90.11381 87.94025 90.70776 assigned negative charge : -357.9827 centred at (gu) : 90.37212 87.54879 90.45531 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23717 grid for indexing accessible points = 1.400000 m= 86903 mr = 123051 m= 31051 mr = 69891 m= 7515 mr = 24082 m= 1069 mr = 5314 m= 71 mr = 656 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 74970 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 18942 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) : 1.891069 object centre at (A) : 11.47400 -20.53050 -1.343500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1858268 0.4864335 midg,1,midg; midg,igrid,midg 0.1871973 9.6092530E-02 1,midg,midg; igrid,midg,midg 4.2390235E-02 0.7478071 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.170000 now iterating at: 14:07:55 rms-change max change #iterations 9.492406 314.5364 at 10iterations 5.596537 126.8112 at 20iterations 3.266111 68.58751 at 30iterations 1.901753 40.43712 at 40iterations 1.106483 21.72968 at 50iterations 0.6411085 13.39685 at 60iterations 0.3708237 7.749083 at 70iterations 0.2143914 4.128308 at 80iterations 0.1242319 2.316851 at 90iterations 7.1615219E-02 1.295303 at 100iterations 4.1222386E-02 0.7666998 at 110iterations 2.3868287E-02 0.4155889 at 120iterations 1.3763490E-02 0.2536697 at 130iterations 7.9586972E-03 0.1452103 at 140iterations 4.6119159E-03 8.8087559E-02 at 150iterations 2.6824593E-03 5.5967093E-02 at 160iterations 1.5760588E-03 2.7749062E-02 at 170iterations 9.4870024E-04 1.8669128E-02 at 180iterations finished qdiffx linear iterations at : 14:08:07 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 9.4870024E-04 1.8669128E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 14:08:08 12.590u 0.200s 0:13.77 92.8% 0+0k 0+0io 0pf+0w