Tue Oct 11 05:27:07 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 05:27:07 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 !!! 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: 0.7169470 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): 25.73200 73.03900 ymin,ymax (A): -20.91100 28.74400 zmin,zma (A): 3.866000 46.49800 x,y,z range (A): 47.30700 49.65500 42.63200 scale (grids/A): 0.7169470 object centre (A): 49.38550 3.916500 25.18200 number of atom coordinates read : 2058 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 88.94238 91.52715 90.12503 assigned negative charge : -304.4261 centred at (gu) : 89.06142 91.39454 90.18126 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7269 nv = 96 ne = 84 npr = 41510 no. pairs analyzed = 41510 no. exposed pairs = 2488 no. arc points = 17015 no. surface atoms = 845 nbur = 1213 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4196 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1596 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7887 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0148626E-07 3.8011656E-08 midg,1,midg; midg,igrid,midg -5.6663096E-09 1.9935632E-07 1,midg,midg; igrid,midg,midg 1.7226786E-07 1.5970632E-10 gauss-seidel spectral radius is 0.9898539 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 05:27:07 rms-change max change #iterations 0.2133168 33.47234 at 10iterations 2.7600897E-02 4.586308 at 20iterations 4.0308819E-03 0.5517054 at 30iterations 8.0427027E-04 9.7877502E-02 at 40iterations 2.3237422E-04 2.6958466E-02 at 50iterations finished qdiffx linear iterations at : 05:27:10 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.3237422E-04 2.6958466E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 05:27:11 3.410u 0.188s 0:04.09 87.7% 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 05:27:11 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 !!! 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: 2.150841 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): 25.73200 73.03900 ymin,ymax (A): -20.91100 28.74400 zmin,zma (A): 3.866000 46.49800 x,y,z range (A): 47.30700 49.65500 42.63200 scale (grids/A): 2.150841 object centre (A): 49.38550 3.916500 25.18200 number of atom coordinates read : 2058 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 86.82720 94.58131 90.37477 assigned negative charge : -304.4261 centred at (gu) : 87.18427 94.18364 90.54400 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17015 grid for indexing accessible points = 1.400000 m= 32091 mr = 54301 m= 6391 mr = 24634 m= 558 mr = 4291 m= 19 mr = 245 m= 0 mr = 0 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 31735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15288 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) : 0.7169470 object centre at (A) : 49.38550 3.916500 25.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2793202E-02 2.7708530E-02 midg,1,midg; midg,igrid,midg 3.3409491E-02 0.1039878 1,midg,midg; igrid,midg,midg 4.5164313E-02 -3.6115170E-02 gauss-seidel spectral radius is 0.9988559 estimated iterations to convergence 234 setup time was (sec) 0.6200000 now iterating at: 05:27:11 rms-change max change #iterations 4.648605 239.0779 at 10iterations 2.316605 74.94894 at 20iterations 1.158498 36.00417 at 30iterations 0.5812161 17.02013 at 40iterations 0.2910542 8.490433 at 50iterations 0.1456653 4.264431 at 60iterations 7.2972104E-02 2.182105 at 70iterations 3.6681555E-02 1.292789 at 80iterations 1.8532034E-02 0.5258980 at 90iterations 9.4666984E-03 0.2797661 at 100iterations 4.8577129E-03 0.1357961 at 110iterations 2.5961297E-03 7.9002380E-02 at 120iterations finished qdiffx linear iterations at : 05:27:19 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.5961297E-03 7.9002380E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 05:27:19 7.889u 0.199s 0:08.36 96.5% 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 Tue Oct 11 2011 at 05:27:19 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2058 !!! 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: 3.226261 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): 25.73200 73.03900 ymin,ymax (A): -20.91100 28.74400 zmin,zma (A): 3.866000 46.49800 x,y,z range (A): 47.30700 49.65500 42.63200 scale (grids/A): 3.226261 object centre (A): 49.38550 3.916500 25.18200 number of atom coordinates read : 2058 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 85.24074 96.87205 90.56228 assigned negative charge : -304.4261 centred at (gu) : 85.77646 96.27560 90.81622 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17015 grid for indexing accessible points = 1.400000 m= 98062 mr = 130560 m= 41774 mr = 82153 m= 12325 mr = 34656 m= 2281 mr = 9561 m= 244 mr = 1582 m= 14 mr = 134 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 15384 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) : 2.150841 object centre at (A) : 49.38550 3.916500 25.18200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1130301 0.2135847 midg,1,midg; midg,igrid,midg 0.2170167 0.8022162 1,midg,midg; igrid,midg,midg 0.3696020 -0.4338763 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 1.470000 now iterating at: 05:27:21 rms-change max change #iterations 10.32442 333.1499 at 10iterations 6.126449 133.6200 at 20iterations 3.635059 71.49598 at 30iterations 2.154057 42.29892 at 40iterations 1.275441 26.31548 at 50iterations 0.7515157 14.60561 at 60iterations 0.4421616 8.673252 at 70iterations 0.2611668 4.801874 at 80iterations 0.1538707 2.974045 at 90iterations 9.0714492E-02 1.778534 at 100iterations 5.3489063E-02 1.100517 at 110iterations 3.1743523E-02 0.5554686 at 120iterations 1.8986588E-02 0.3205376 at 130iterations 1.1601173E-02 0.2202492 at 140iterations 7.3051364E-03 0.1394997 at 150iterations 4.8128380E-03 8.4548950E-02 at 160iterations 3.3733398E-03 6.2500000E-02 at 170iterations 2.5034561E-03 4.5207977E-02 at 180iterations finished qdiffx linear iterations at : 05:27:32 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 2.5034561E-03 4.5207977E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 05:27:33 13.029u 0.195s 0:13.73 96.2% 0+0k 0+0io 0pf+0w