Sat Oct 8 11:33:56 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+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 Sat Oct 8 2011 at 11:33:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5761357 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): -25.74200 36.04900 ymin,ymax (A): 37.30500 95.23400 zmin,zma (A): 30.75500 87.85400 x,y,z range (A): 61.79100 57.92900 57.09901 scale (grids/A): 0.5761357 object centre (A): 5.153501 66.26950 59.30450 number of atom coordinates read : 4399 total number of charged atoms : 4246 net assigned charge : 3.9860606E-05 assigned positive charge : 659.9944 centred at (gu) : 90.51099 88.69736 88.94899 assigned negative charge : -659.9973 centred at (gu) : 90.36315 88.87177 89.10255 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 9272 nv = 96 ne = 84 npr = 93306 no. pairs analyzed = 93306 no. exposed pairs = 4872 no. arc points = 33066 no. surface atoms = 1655 nbur = 2744 mkacc time = 0.1600000 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= 401 mr = 5428 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.3100000 number of dielectric boundary points 4213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3539 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 12328 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3932405E-09 -3.5978553E-09 midg,1,midg; midg,igrid,midg 6.5206991E-09 -3.8455172E-09 1,midg,midg; igrid,midg,midg -3.9404267E-09 4.5536197E-09 gauss-seidel spectral radius is 0.9845500 estimated iterations to convergence 66 setup time was (sec) 0.5100000 now iterating at: 11:33:57 rms-change max change #iterations 0.1163892 15.57368 at 10iterations 9.3141049E-03 1.236649 at 20iterations 8.6494331E-04 0.1009521 at 30iterations 1.4761608E-04 1.9746780E-02 at 40iterations 4.4525776E-05 6.0954094E-03 at 50iterations finished qdiffx linear iterations at : 11:34:00 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 4.4525776E-05 6.0954094E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 11:34:01 3.581u 0.230s 0:04.15 91.8% 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 Sat Oct 8 2011 at 11:34:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.728407 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): -25.74200 36.04900 ymin,ymax (A): 37.30500 95.23400 zmin,zma (A): 30.75500 87.85400 x,y,z range (A): 61.79100 57.92900 57.09901 scale (grids/A): 1.728407 object centre (A): 5.153501 66.26950 59.30450 number of atom coordinates read : 4399 total number of charged atoms : 4246 net assigned charge : 3.9860606E-05 assigned positive charge : 659.9944 centred at (gu) : 91.53144 86.09093 86.84547 assigned negative charge : -659.9973 centred at (gu) : 91.08913 86.61511 87.30721 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103671 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33066 grid for indexing accessible points = 1.400000 m= 34959 mr = 75661 m= 4407 mr = 25865 m= 142 mr = 2630 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 6832 time to turn everything in is 0.4900000 number of dielectric boundary points 39007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 32887 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) : 0.5761357 object centre at (A) : 5.153501 66.26950 59.30450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8287483E-02 -3.2220855E-02 midg,1,midg; midg,igrid,midg 3.8887981E-02 -1.7262755E-02 1,midg,midg; igrid,midg,midg -1.4453093E-02 4.1792415E-02 gauss-seidel spectral radius is 0.9985057 estimated iterations to convergence 205 setup time was (sec) 0.7100000 now iterating at: 11:34:02 rms-change max change #iterations 4.716087 193.0524 at 10iterations 2.133526 60.61533 at 20iterations 0.9639267 28.19097 at 30iterations 0.4372579 13.19278 at 40iterations 0.1978841 5.102736 at 50iterations 9.0113647E-02 2.587612 at 60iterations 4.0725190E-02 1.083941 at 70iterations 1.8501434E-02 0.5243199 at 80iterations 8.4309876E-03 0.2463074 at 90iterations 3.8368443E-03 0.1034784 at 100iterations 1.7560641E-03 4.8352242E-02 at 110iterations 8.1307872E-04 2.3268700E-02 at 120iterations finished qdiffx linear iterations at : 11:34:09 total time elapsed so far: 8.090000 # loops : 120 mean,max change (kT/e) : 8.1307872E-04 2.3268700E-02 energy calculations done at 8.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.220000 DelPhi exited at 11:34:09 8.223u 0.221s 0:08.83 95.5% 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 8 2011 at 11:34:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.592611 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): -25.74200 36.04900 ymin,ymax (A): 37.30500 95.23400 zmin,zma (A): 30.75500 87.85400 x,y,z range (A): 61.79100 57.92900 57.09901 scale (grids/A): 2.592611 object centre (A): 5.153501 66.26950 59.30450 number of atom coordinates read : 4399 total number of charged atoms : 4246 net assigned charge : 3.9860606E-05 assigned positive charge : 659.9944 centred at (gu) : 92.29699 84.13618 85.26795 assigned negative charge : -659.9973 centred at (gu) : 91.63354 84.92258 85.96067 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 241083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33066 grid for indexing accessible points = 1.400000 m= 119077 mr = 183831 m= 37385 mr = 98378 m= 7490 mr = 29748 m= 765 mr = 5527 m= 16 mr = 426 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 22858 time to turn everything in is 1.240000 number of dielectric boundary points 87906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 33955 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) : 1.728407 object centre at (A) : 5.153501 66.26950 59.30450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6423934 -0.4315470 midg,1,midg; midg,igrid,midg 0.4583937 -0.2436092 1,midg,midg; igrid,midg,midg -0.2246838 0.4517788 gauss-seidel spectral radius is 0.9992501 estimated iterations to convergence 288 setup time was (sec) 1.490000 now iterating at: 11:34:11 rms-change max change #iterations 11.59873 302.6044 at 10iterations 6.779264 130.4455 at 20iterations 3.937610 74.93040 at 30iterations 2.283486 43.41489 at 40iterations 1.315556 22.42602 at 50iterations 0.7605781 13.55911 at 60iterations 0.4381664 7.012246 at 70iterations 0.2518072 4.300665 at 80iterations 0.1448836 2.342086 at 90iterations 8.3062470E-02 1.330758 at 100iterations 4.7728963E-02 0.8412874 at 110iterations 2.7410198E-02 0.4642143 at 120iterations 1.5712520E-02 0.2684879 at 130iterations 9.0528075E-03 0.1468592 at 140iterations 5.1971874E-03 8.4407806E-02 at 150iterations 3.0022969E-03 4.6848297E-02 at 160iterations 1.7402102E-03 2.9345512E-02 at 170iterations 1.0234627E-03 1.6010284E-02 at 180iterations finished qdiffx linear iterations at : 11:34:23 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 1.0234627E-03 1.6010284E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.76000 DelPhi exited at 11:34:24 13.764u 0.262s 0:14.47 96.8% 0+0k 0+0io 0pf+0w