Sat Oct 15 14:32:56 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 14:33:02 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5660588 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): -30.18600 32.70500 ymin,ymax (A): -22.35500 25.42000 zmin,zma (A): -8.047999 40.16800 x,y,z range (A): 62.89100 47.77500 48.21600 scale (grids/A): 0.5660588 object centre (A): 1.259500 1.532500 16.06000 number of atom coordinates read : 2758 total number of charged atoms : 2619 net assigned charge : -1.485970 assigned positive charge : 415.4823 centred at (gu) : 90.11974 90.30504 89.76402 assigned negative charge : -416.9693 centred at (gu) : 90.12309 90.20255 89.72682 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5807 nv = 96 ne = 84 npr = 55089 no. pairs analyzed = 55089 no. exposed pairs = 3606 no. arc points = 25547 no. surface atoms = 1214 nbur = 1544 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 269 mr = 3009 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2544 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7477 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2106654E-10 2.6055264E-10 midg,1,midg; midg,igrid,midg -1.4268514E-09 1.1887682E-09 1,midg,midg; igrid,midg,midg -1.5273285E-10 -2.5034586E-10 gauss-seidel spectral radius is 0.9838829 estimated iterations to convergence 65 setup time was (sec) 0.4700000 now iterating at: 14:33:04 rms-change max change #iterations 8.5016713E-02 18.45731 at 10iterations 6.0761841E-03 1.114582 at 20iterations 4.6232191E-04 8.1232071E-02 at 30iterations 3.3752745E-05 5.3689480E-03 at 40iterations 2.4160615E-06 4.0054321E-04 at 50iterations finished qdiffx linear iterations at : 14:33:08 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.4160615E-06 4.0054321E-04 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 14:33:09 3.126u 0.163s 0:08.32 39.4% 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 14:33:12 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.698176 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): -30.18600 32.70500 ymin,ymax (A): -22.35500 25.42000 zmin,zma (A): -8.047999 40.16800 x,y,z range (A): 62.89100 47.77500 48.21600 scale (grids/A): 1.698176 object centre (A): 1.259500 1.532500 16.06000 number of atom coordinates read : 2758 total number of charged atoms : 2619 net assigned charge : -1.485970 assigned positive charge : 415.4823 centred at (gu) : 90.35868 90.91432 89.29118 assigned negative charge : -416.9693 centred at (gu) : 90.36889 90.60721 89.18020 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 64114 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25547 grid for indexing accessible points = 1.400000 m= 19659 mr = 43147 m= 2110 mr = 13445 m= 64 mr = 1011 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 253 time to turn everything in is 0.4300000 number of dielectric boundary points 28338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 273 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 20230 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) : 0.5660588 object centre at (A) : 1.259500 1.532500 16.06000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4414885E-03 -2.4382262E-03 midg,1,midg; midg,igrid,midg -1.6366076E-02 7.9199886E-03 1,midg,midg; igrid,midg,midg 5.2209026E-03 1.9270238E-02 gauss-seidel spectral radius is 0.9983025 estimated iterations to convergence 193 setup time was (sec) 0.7000000 now iterating at: 14:33:14 rms-change max change #iterations 3.508898 188.3217 at 10iterations 1.499442 53.33617 at 20iterations 0.6409916 23.98101 at 30iterations 0.2757214 10.32583 at 40iterations 0.1176616 4.165552 at 50iterations 5.0664436E-02 1.969237 at 60iterations 2.1671752E-02 0.7875028 at 70iterations 9.2571890E-03 0.3579788 at 80iterations 3.9760293E-03 0.1443882 at 90iterations 1.7058703E-03 6.7896843E-02 at 100iterations 7.3096366E-04 3.0317307E-02 at 110iterations 3.1568739E-04 1.1543274E-02 at 120iterations finished qdiffx linear iterations at : 14:33:28 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 3.1568739E-04 1.1543274E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 14:33:30 6.872u 0.183s 0:18.78 37.5% 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 14:33:32 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2758 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.547264 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): -30.18600 32.70500 ymin,ymax (A): -22.35500 25.42000 zmin,zma (A): -8.047999 40.16800 x,y,z range (A): 62.89100 47.77500 48.21600 scale (grids/A): 2.547264 object centre (A): 1.259500 1.532500 16.06000 number of atom coordinates read : 2758 total number of charged atoms : 2619 net assigned charge : -1.485970 assigned positive charge : 415.4823 centred at (gu) : 90.53781 91.37138 88.93654 assigned negative charge : -416.9693 centred at (gu) : 90.55328 90.91071 88.77022 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 148740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25547 grid for indexing accessible points = 1.400000 m= 68054 mr = 105638 m= 19507 mr = 53586 m= 3296 mr = 14485 m= 243 mr = 2097 m= 6 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 863 time to turn everything in is 1.030000 number of dielectric boundary points 63927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 20942 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) : 1.698176 object centre at (A) : 1.259500 1.532500 16.06000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0990137E-02 -5.4139633E-02 midg,1,midg; midg,igrid,midg -0.2034984 0.1408079 1,midg,midg; igrid,midg,midg 0.2584214 0.3510015 gauss-seidel spectral radius is 0.9991703 estimated iterations to convergence 274 setup time was (sec) 1.300000 now iterating at: 14:33:36 rms-change max change #iterations 8.875040 302.9318 at 10iterations 5.026897 135.2734 at 20iterations 2.839304 68.69780 at 30iterations 1.597283 38.29632 at 40iterations 0.8932724 19.39597 at 50iterations 0.5006484 10.37384 at 60iterations 0.2790061 6.170227 at 70iterations 0.1554254 3.380768 at 80iterations 8.6455360E-02 1.949123 at 90iterations 4.8185650E-02 1.074264 at 100iterations 2.6762011E-02 0.5613327 at 110iterations 1.4840023E-02 0.2893372 at 120iterations 8.2494216E-03 0.1685529 at 130iterations 4.5857700E-03 0.1048203 at 140iterations 2.5472720E-03 5.5532426E-02 at 150iterations 1.4105618E-03 2.8005600E-02 at 160iterations 7.8467763E-04 1.6661167E-02 at 170iterations 4.3508247E-04 8.9416504E-03 at 180iterations finished qdiffx linear iterations at : 14:33:45 total time elapsed so far: 10.83000 # loops : 180 mean,max change (kT/e) : 4.3508247E-04 8.9416504E-03 energy calculations done at 10.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.00000 DelPhi exited at 14:33:46 11.003u 0.205s 0:14.09 79.4% 0+0k 0+0io 0pf+0w