Sun Oct 9 15:09:13 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 Sun Oct 9 2011 at 15:09:13 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5016416 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): 33.44200 104.4090 ymin,ymax (A): -10.17900 56.89600 zmin,zma (A): -34.67500 32.70200 x,y,z range (A): 70.96700 67.07500 67.37700 scale (grids/A): 0.5016416 object centre (A): 68.92550 23.35850 -0.9864998 number of atom coordinates read : 5360 total number of charged atoms : 5188 net assigned charge : -4.499959 assigned positive charge : 820.0554 centred at (gu) : 90.87164 90.89521 89.74387 assigned negative charge : -824.5619 centred at (gu) : 90.92329 90.81727 89.69250 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8161 nv = 96 ne = 84 npr = 109695 no. pairs analyzed = 109695 no. exposed pairs = 6387 no. arc points = 43517 no. surface atoms = 2139 nbur = 3221 mkacc time = 0.2300000 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 = 1.708000 m= 298 mr = 4375 m= 4 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.5000000 number of dielectric boundary points 4073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4179 ## 649 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 11144 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5797379E-10 5.6482628E-11 midg,1,midg; midg,igrid,midg -1.5906523E-10 1.4562825E-10 1,midg,midg; igrid,midg,midg 4.8035308E-11 -1.8733845E-10 gauss-seidel spectral radius is 0.9797090 estimated iterations to convergence 58 setup time was (sec) 0.7200000 now iterating at: 15:09:14 rms-change max change #iterations 6.7529924E-02 10.58563 at 10iterations 5.6280084E-03 0.9931870 at 20iterations 1.4444598E-03 0.2769814 at 30iterations 4.6679750E-04 8.9828491E-02 at 40iterations 1.5286857E-04 2.9258728E-02 at 50iterations finished qdiffx linear iterations at : 15:09:17 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 1.5286857E-04 2.9258728E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 15:09:17 3.350u 0.131s 0:03.79 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 Sun Oct 9 2011 at 15:09:17 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.504925 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): 33.44200 104.4090 ymin,ymax (A): -10.17900 56.89600 zmin,zma (A): -34.67500 32.70200 x,y,z range (A): 70.96700 67.07500 67.37700 scale (grids/A): 1.504925 object centre (A): 68.92550 23.35850 -0.9864998 number of atom coordinates read : 5360 total number of charged atoms : 5188 net assigned charge : -4.499959 assigned positive charge : 820.0554 centred at (gu) : 92.61291 92.68385 89.23005 assigned negative charge : -824.5619 centred at (gu) : 92.76939 92.45129 89.07733 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 93210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43517 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27127 mr = 65112 m= 2450 mr = 18368 m= 53 mr = 1067 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1675 time to turn everything in is 0.6400000 number of dielectric boundary points 38293 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 601 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 38658 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) : 0.5016416 object centre at (A) : 68.92550 23.35850 -0.9864998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5988025E-05 -7.6213554E-03 midg,1,midg; midg,igrid,midg -1.3188221E-02 1.7042937E-02 1,midg,midg; igrid,midg,midg 5.8174613E-03 -5.3159900E-02 gauss-seidel spectral radius is 0.9980720 estimated iterations to convergence 181 setup time was (sec) 0.9100000 now iterating at: 15:09:18 rms-change max change #iterations 3.923291 171.5709 at 10iterations 1.596637 53.02142 at 20iterations 0.6493817 20.59126 at 30iterations 0.2639963 8.543514 at 40iterations 0.1079868 4.121006 at 50iterations 4.4223342E-02 1.361378 at 60iterations 1.8448811E-02 0.5807037 at 70iterations 7.9117706E-03 0.2535019 at 80iterations 3.6321827E-03 0.1281586 at 90iterations 1.8544961E-03 7.4451447E-02 at 100iterations 1.0655383E-03 4.1793823E-02 at 110iterations 6.6687114E-04 2.7091980E-02 at 120iterations finished qdiffx linear iterations at : 15:09:24 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 6.6687114E-04 2.7091980E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 15:09:25 7.070u 0.161s 0:07.52 96.1% 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 15:09:25 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5360 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.257387 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): 33.44200 104.4090 ymin,ymax (A): -10.17900 56.89600 zmin,zma (A): -34.67500 32.70200 x,y,z range (A): 70.96700 67.07500 67.37700 scale (grids/A): 2.257387 object centre (A): 68.92550 23.35850 -0.9864998 number of atom coordinates read : 5360 total number of charged atoms : 5188 net assigned charge : -4.499959 assigned positive charge : 820.0554 centred at (gu) : 93.91894 94.02544 88.84451 assigned negative charge : -824.5619 centred at (gu) : 94.15411 93.67705 88.61595 start vw surface at 0.2100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 217740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43517 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 97221 mr = 160231 m= 25146 mr = 76399 m= 3605 mr = 18414 m= 159 mr = 2251 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 5778 time to turn everything in is 1.510000 number of dielectric boundary points 86545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 41354 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) : 1.504925 object centre at (A) : 68.92550 23.35850 -0.9864998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4762774E-02 -0.1757783 midg,1,midg; midg,igrid,midg -0.2120421 0.4849572 1,midg,midg; igrid,midg,midg 0.2881245 -1.326667 gauss-seidel spectral radius is 0.9991553 estimated iterations to convergence 272 setup time was (sec) 1.800000 now iterating at: 15:09:27 rms-change max change #iterations 10.74974 286.6019 at 10iterations 6.099962 138.8869 at 20iterations 3.456000 75.79205 at 30iterations 1.940576 42.30511 at 40iterations 1.085424 21.51526 at 50iterations 0.6068411 11.76521 at 60iterations 0.3381903 7.896776 at 70iterations 0.1884010 3.724010 at 80iterations 0.1046447 1.995399 at 90iterations 5.8137663E-02 1.128296 at 100iterations 3.2293417E-02 0.5925217 at 110iterations 1.7947640E-02 0.3177967 at 120iterations 9.9710617E-03 0.2070885 at 130iterations 5.5739935E-03 9.9372864E-02 at 140iterations 3.1347517E-03 5.6777954E-02 at 150iterations 1.7790195E-03 3.3199310E-02 at 160iterations 1.0327558E-03 1.9340515E-02 at 170iterations 6.1824481E-04 1.2939453E-02 at 180iterations finished qdiffx linear iterations at : 15:09:36 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 6.1824481E-04 1.2939453E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 15:09:37 11.556u 0.164s 0:11.99 97.6% 0+0k 0+0io 0pf+0w