Sun Oct 9 19:53:16 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+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 Sun Oct 9 2011 at 19:53:16 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5693085 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): 6.472000 66.52400 ymin,ymax (A): 1.702000 61.88100 zmin,zma (A): -0.6970000 61.83500 x,y,z range (A): 60.05200 60.17900 62.53200 scale (grids/A): 0.5693085 object centre (A): 36.49800 31.79150 30.56900 number of atom coordinates read : 3514 total number of charged atoms : 3365 net assigned charge : -0.3789752 assigned positive charge : 530.6765 centred at (gu) : 88.65665 88.36366 88.79568 assigned negative charge : -531.0575 centred at (gu) : 88.61205 88.43041 88.75822 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7776 nv = 96 ne = 84 npr = 66762 no. pairs analyzed = 66762 no. exposed pairs = 4771 no. arc points = 33407 no. surface atoms = 1604 nbur = 1910 mkacc time = 0.1400000 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= 389 mr = 3989 m= 0 mr = 22 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3290 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.9425357E-10 4.6498433E-10 midg,1,midg; midg,igrid,midg 1.7162033E-09 -8.6589785E-10 1,midg,midg; igrid,midg,midg -1.2108680E-09 5.4280902E-10 gauss-seidel spectral radius is 0.9841334 estimated iterations to convergence 65 setup time was (sec) 0.6200000 now iterating at: 19:53:17 rms-change max change #iterations 9.8327957E-02 16.96398 at 10iterations 7.6323622E-03 1.049461 at 20iterations 1.0366521E-03 0.1448212 at 30iterations 5.1577279E-04 5.5744171E-02 at 40iterations 3.2607693E-04 3.6775112E-02 at 50iterations finished qdiffx linear iterations at : 19:53:20 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 3.2607693E-04 3.6775112E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 19:53:20 3.492u 0.205s 0:04.02 91.7% 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 Sun Oct 9 2011 at 19:53:20 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.707926 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): 6.472000 66.52400 ymin,ymax (A): 1.702000 61.88100 zmin,zma (A): -0.6970000 61.83500 x,y,z range (A): 60.05200 60.17900 62.53200 scale (grids/A): 1.707926 object centre (A): 36.49800 31.79150 30.56900 number of atom coordinates read : 3514 total number of charged atoms : 3365 net assigned charge : -0.3789752 assigned positive charge : 530.6765 centred at (gu) : 85.96858 85.08961 86.38602 assigned negative charge : -531.0575 centred at (gu) : 85.83569 85.29087 86.27411 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85200 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33407 grid for indexing accessible points = 1.400000 m= 29631 mr = 57825 m= 4011 mr = 20507 m= 158 mr = 2166 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 38482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 26075 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) : 0.5693085 object centre at (A) : 36.49800 31.79150 30.56900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1650707E-02 -1.0466707E-02 midg,1,midg; midg,igrid,midg 1.7708037E-02 -4.6785148E-03 1,midg,midg; igrid,midg,midg -4.2251828E-03 2.7354591E-04 gauss-seidel spectral radius is 0.9984130 estimated iterations to convergence 199 setup time was (sec) 0.9300000 now iterating at: 19:53:21 rms-change max change #iterations 4.127573 168.2222 at 10iterations 1.828270 64.97977 at 20iterations 0.8109046 29.52745 at 30iterations 0.3585592 11.47531 at 40iterations 0.1586587 5.003675 at 50iterations 7.0548579E-02 2.186928 at 60iterations 3.1312775E-02 1.208765 at 70iterations 1.3887423E-02 0.4657059 at 80iterations 6.2449994E-03 0.1869910 at 90iterations 2.8753912E-03 9.4075203E-02 at 100iterations 1.4339196E-03 4.7027588E-02 at 110iterations 8.4468117E-04 2.5501251E-02 at 120iterations finished qdiffx linear iterations at : 19:53:28 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 8.4468117E-04 2.5501251E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 19:53:29 7.848u 0.228s 0:08.40 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 Sun Oct 9 2011 at 19:53:29 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.561888 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): 6.472000 66.52400 ymin,ymax (A): 1.702000 61.88100 zmin,zma (A): -0.6970000 61.83500 x,y,z range (A): 60.05200 60.17900 62.53200 scale (grids/A): 2.561888 object centre (A): 36.49800 31.79150 30.56900 number of atom coordinates read : 3514 total number of charged atoms : 3365 net assigned charge : -0.3789752 assigned positive charge : 530.6765 centred at (gu) : 83.95251 82.63405 84.57858 assigned negative charge : -531.0575 centred at (gu) : 83.75350 82.93616 84.41122 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 197345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33407 grid for indexing accessible points = 1.400000 m= 97910 mr = 141290 m= 32675 mr = 77406 m= 6863 mr = 24800 m= 596 mr = 4628 m= 17 mr = 288 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 86994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 26903 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) : 1.707926 object centre at (A) : 36.49800 31.79150 30.56900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2069342 -5.6053154E-02 midg,1,midg; midg,igrid,midg 0.2004086 -6.8989195E-02 1,midg,midg; igrid,midg,midg 1.3994185E-02 -1.4699594E-02 gauss-seidel spectral radius is 0.9992297 estimated iterations to convergence 284 setup time was (sec) 1.800000 now iterating at: 19:53:31 rms-change max change #iterations 10.65745 342.0776 at 10iterations 6.368478 158.0969 at 20iterations 3.746397 95.96887 at 30iterations 2.187060 45.92170 at 40iterations 1.271899 27.90425 at 50iterations 0.7362852 17.32417 at 60iterations 0.4254704 8.396255 at 70iterations 0.2443975 4.858059 at 80iterations 0.1403985 2.876753 at 90iterations 8.0783106E-02 1.721764 at 100iterations 4.6235852E-02 0.8670013 at 110iterations 2.6531929E-02 0.5057926 at 120iterations 1.5148619E-02 0.2935705 at 130iterations 8.6753666E-03 0.1738548 at 140iterations 4.9656816E-03 9.3833923E-02 at 150iterations 2.8462298E-03 5.5290222E-02 at 160iterations 1.6489098E-03 3.1829834E-02 at 170iterations 9.6851436E-04 2.0877838E-02 at 180iterations finished qdiffx linear iterations at : 19:53:43 total time elapsed so far: 14.46000 # loops : 180 mean,max change (kT/e) : 9.6851436E-04 2.0877838E-02 energy calculations done at 14.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.66000 DelPhi exited at 19:53:44 14.657u 0.255s 0:15.21 97.9% 0+0k 0+0io 0pf+0w