Tue Oct 11 05:49:16 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 05:49:16 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7193372 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): 3.519000 47.79200 ymin,ymax (A): 1.785000 39.30300 zmin,zma (A): -2.754000 46.73600 x,y,z range (A): 44.27300 37.51800 49.49000 scale (grids/A): 0.7193372 object centre (A): 25.65550 20.54400 21.99100 number of atom coordinates read : 2232 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.2071 centred at (gu) : 89.72317 90.78332 90.56538 assigned negative charge : -304.2762 centred at (gu) : 89.92266 90.77852 90.57726 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7199 nv = 96 ne = 84 npr = 41686 no. pairs analyzed = 41686 no. exposed pairs = 2474 no. arc points = 16739 no. surface atoms = 841 nbur = 1391 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4188 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3397 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1497 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7864 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5884721E-08 7.7010121E-08 midg,1,midg; midg,igrid,midg 6.3945329E-08 9.2380255E-08 1,midg,midg; igrid,midg,midg 2.1016720E-07 -4.7567511E-08 gauss-seidel spectral radius is 0.9899188 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 05:49:16 rms-change max change #iterations 0.2130008 30.00776 at 10iterations 2.7704366E-02 4.010416 at 20iterations 3.7515857E-03 0.5131683 at 30iterations 6.3974597E-04 8.7600708E-02 at 40iterations 1.4997531E-04 1.8386841E-02 at 50iterations finished qdiffx linear iterations at : 05:49:19 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.4997531E-04 1.8386841E-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) 3.380000 DelPhi exited at 05:49:20 3.384u 0.174s 0:03.93 90.3% 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 05:49:20 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.158012 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): 3.519000 47.79200 ymin,ymax (A): 1.785000 39.30300 zmin,zma (A): -2.754000 46.73600 x,y,z range (A): 44.27300 37.51800 49.49000 scale (grids/A): 2.158012 object centre (A): 25.65550 20.54400 21.99100 number of atom coordinates read : 2232 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.2071 centred at (gu) : 89.16960 92.35000 91.69622 assigned negative charge : -304.2762 centred at (gu) : 89.76795 92.33580 91.73188 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76169 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16739 grid for indexing accessible points = 1.400000 m= 30666 mr = 54485 m= 6116 mr = 23431 m= 652 mr = 4177 m= 12 mr = 350 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15193 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) : 0.7193372 object centre at (A) : 25.65550 20.54400 21.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5629332E-02 7.7583253E-02 midg,1,midg; midg,igrid,midg 6.4886920E-03 3.5012569E-02 1,midg,midg; igrid,midg,midg 5.3553738E-02 1.7007457E-03 gauss-seidel spectral radius is 0.9988592 estimated iterations to convergence 234 setup time was (sec) 0.6100000 now iterating at: 05:49:20 rms-change max change #iterations 4.690293 244.2365 at 10iterations 2.341323 69.66244 at 20iterations 1.175034 33.18262 at 30iterations 0.5867353 17.05174 at 40iterations 0.2952989 9.412200 at 50iterations 0.1480428 4.537529 at 60iterations 7.4213035E-02 2.093542 at 70iterations 3.7243202E-02 1.172889 at 80iterations 1.8757245E-02 0.5663681 at 90iterations 9.5047569E-03 0.2951660 at 100iterations 4.8209769E-03 0.1433532 at 110iterations 2.4979892E-03 7.6375961E-02 at 120iterations finished qdiffx linear iterations at : 05:49:28 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.4979892E-03 7.6375961E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 05:49:28 7.868u 0.197s 0:08.39 95.9% 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 Tue Oct 11 2011 at 05:49:28 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2232 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.237017 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): 3.519000 47.79200 ymin,ymax (A): 1.785000 39.30300 zmin,zma (A): -2.754000 46.73600 x,y,z range (A): 44.27300 37.51800 49.49000 scale (grids/A): 3.237017 object centre (A): 25.65550 20.54400 21.99100 number of atom coordinates read : 2232 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.2071 centred at (gu) : 88.75443 93.52496 92.54426 assigned negative charge : -304.2762 centred at (gu) : 89.65199 93.50377 92.59784 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16739 grid for indexing accessible points = 1.400000 m= 95760 mr = 131290 m= 38999 mr = 80010 m= 11545 mr = 32152 m= 2459 mr = 8991 m= 301 mr = 1844 m= 7 mr = 210 m= 0 mr = 2 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70279 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 15379 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) : 2.158012 object centre at (A) : 25.65550 20.54400 21.99100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2699481 0.7180794 midg,1,midg; midg,igrid,midg 1.9772824E-02 0.2647150 1,midg,midg; igrid,midg,midg 0.4192162 0.1069989 gauss-seidel spectral radius is 0.9992999 estimated iterations to convergence 298 setup time was (sec) 1.420000 now iterating at: 05:49:30 rms-change max change #iterations 10.39006 329.1642 at 10iterations 6.148789 130.2438 at 20iterations 3.640666 76.90663 at 30iterations 2.148718 41.86096 at 40iterations 1.267422 22.15090 at 50iterations 0.7442669 13.30902 at 60iterations 0.4386331 7.989806 at 70iterations 0.2574647 4.565495 at 80iterations 0.1513827 2.754107 at 90iterations 8.9095250E-02 1.787445 at 100iterations 5.2502532E-02 0.8983612 at 110iterations 3.1007903E-02 0.5589485 at 120iterations 1.8545968E-02 0.3571587 at 130iterations 1.1247781E-02 0.2084961 at 140iterations 7.0420066E-03 0.1283493 at 150iterations 4.5921155E-03 8.1218719E-02 at 160iterations 3.1487937E-03 5.6198120E-02 at 170iterations 2.2916549E-03 3.7181854E-02 at 180iterations finished qdiffx linear iterations at : 05:49:41 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.2916549E-03 3.7181854E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 05:49:41 12.898u 0.212s 0:13.39 97.8% 0+0k 0+0io 0pf+0w