Sat Oct 15 13:39:58 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 13:40:02 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 0.6592715 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): 20.40200 67.98700 ymin,ymax (A): 39.24100 93.24000 zmin,zma (A): 44.80800 95.82600 x,y,z range (A): 47.58500 53.99900 51.01799 scale (grids/A): 0.6592715 object centre (A): 44.19450 66.24049 70.31700 number of atom coordinates read : 2358 total number of charged atoms : 2209 net assigned charge : -18.99998 assigned positive charge : 361.1575 centred at (gu) : 89.57002 89.85606 89.40134 assigned negative charge : -380.1577 centred at (gu) : 89.44301 89.97826 89.57423 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7040 nv = 96 ne = 84 npr = 46674 no. pairs analyzed = 46674 no. exposed pairs = 3268 no. arc points = 23899 no. surface atoms = 1080 nbur = 1278 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 418 mr = 3577 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 93 time to turn everything in is 0.3200000 number of dielectric boundary points 3848 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8157 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6816287E-08 -7.1583059E-08 midg,1,midg; midg,igrid,midg -2.5156822E-08 -6.8921373E-08 1,midg,midg; igrid,midg,midg -7.8563225E-08 -2.1749964E-08 gauss-seidel spectral radius is 0.9880660 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 13:40:06 rms-change max change #iterations 0.1647583 37.45546 at 10iterations 1.7110988E-02 2.960434 at 20iterations 1.8245379E-03 0.2684917 at 30iterations 1.9373848E-04 2.9411316E-02 at 40iterations 2.0244946E-05 3.0164719E-03 at 50iterations finished qdiffx linear iterations at : 13:40:15 total time elapsed so far: 3.750000 # loops : 50 mean,max change (kT/e) : 2.0244946E-05 3.0164719E-03 energy calculations done at 3.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.990000 DelPhi exited at 13:40:17 3.993u 0.154s 0:15.20 27.2% 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 13:40:20 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 1.977814 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): 20.40200 67.98700 ymin,ymax (A): 39.24100 93.24000 zmin,zma (A): 44.80800 95.82600 x,y,z range (A): 47.58500 53.99900 51.01799 scale (grids/A): 1.977814 object centre (A): 44.19450 66.24049 70.31700 number of atom coordinates read : 2358 total number of charged atoms : 2209 net assigned charge : -18.99998 assigned positive charge : 361.1575 centred at (gu) : 88.70986 89.56785 88.20360 assigned negative charge : -380.1577 centred at (gu) : 88.32880 89.93451 88.72237 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 74857 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23899 grid for indexing accessible points = 1.400000 m= 26525 mr = 48994 m= 4054 mr = 18722 m= 220 mr = 2328 m= 4 mr = 82 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2207 time to turn everything in is 0.6800000 number of dielectric boundary points 35534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 129 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 17488 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) : 0.6592715 object centre at (A) : 44.19450 66.24049 70.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7003845E-03 -5.5835910E-02 midg,1,midg; midg,igrid,midg -0.1379644 -0.1414923 1,midg,midg; igrid,midg,midg -3.9857276E-02 -2.4957273E-03 gauss-seidel spectral radius is 0.9987210 estimated iterations to convergence 221 setup time was (sec) 1.030000 now iterating at: 13:40:26 rms-change max change #iterations 4.530475 193.9572 at 10iterations 2.161113 80.70107 at 20iterations 1.027962 33.86379 at 30iterations 0.4930504 15.61581 at 40iterations 0.2356191 7.568085 at 50iterations 0.1129213 3.661440 at 60iterations 5.4075874E-02 1.723831 at 70iterations 2.5810113E-02 0.7821541 at 80iterations 1.2355368E-02 0.3922119 at 90iterations 5.9149317E-03 0.1947680 at 100iterations 2.8289866E-03 8.7528229E-02 at 110iterations 1.3537996E-03 4.6449661E-02 at 120iterations finished qdiffx linear iterations at : 13:40:49 total time elapsed so far: 8.850000 # loops : 120 mean,max change (kT/e) : 1.3537996E-03 4.6449661E-02 energy calculations done at 8.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.080000 DelPhi exited at 13:40:52 9.081u 0.170s 0:33.03 28.0% 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 13:40:57 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 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: 2.966722 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): 20.40200 67.98700 ymin,ymax (A): 39.24100 93.24000 zmin,zma (A): 44.80800 95.82600 x,y,z range (A): 47.58500 53.99900 51.01799 scale (grids/A): 2.966722 object centre (A): 44.19450 66.24049 70.31700 number of atom coordinates read : 2358 total number of charged atoms : 2209 net assigned charge : -18.99998 assigned positive charge : 361.1575 centred at (gu) : 88.06461 89.35174 87.30542 assigned negative charge : -380.1577 centred at (gu) : 87.49315 89.90174 88.08348 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 172834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23899 grid for indexing accessible points = 1.400000 m= 84877 mr = 119333 m= 30530 mr = 67498 m= 7161 mr = 23759 m= 962 mr = 5058 m= 77 mr = 596 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 7544 time to turn everything in is 1.720000 number of dielectric boundary points 80177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 17672 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) : 1.977814 object centre at (A) : 44.19450 66.24049 70.31700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1751567 -0.7826284 midg,1,midg; midg,igrid,midg -1.827138 -1.218228 1,midg,midg; igrid,midg,midg -0.2685468 3.5555318E-02 gauss-seidel spectral radius is 0.9992802 estimated iterations to convergence 294 setup time was (sec) 2.080000 now iterating at: 13:41:05 rms-change max change #iterations 10.42517 363.7238 at 10iterations 6.075791 133.9537 at 20iterations 3.526957 76.49590 at 30iterations 2.045830 44.13236 at 40iterations 1.187034 23.14993 at 50iterations 0.6873734 12.27913 at 60iterations 0.3984125 8.384516 at 70iterations 0.2297322 4.334780 at 80iterations 0.1331708 2.446291 at 90iterations 7.6879218E-02 1.569598 at 100iterations 4.4409275E-02 0.7963972 at 110iterations 2.5731079E-02 0.4914513 at 120iterations 1.4835411E-02 0.2456445 at 130iterations 8.6008972E-03 0.1596843 at 140iterations 4.9614343E-03 9.3545914E-02 at 150iterations 2.8650970E-03 5.1044464E-02 at 160iterations 1.6554904E-03 3.2375336E-02 at 170iterations 9.6078194E-04 1.8314362E-02 at 180iterations finished qdiffx linear iterations at : 13:41:59 total time elapsed so far: 16.28000 # loops : 180 mean,max change (kT/e) : 9.6078194E-04 1.8314362E-02 energy calculations done at 16.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 13:42:02 16.504u 0.209s 1:05.23 25.6% 0+0k 0+0io 0pf+0w