Tue Oct 11 07:40:09 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 07:40:09 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIQ 56 has a net charge of 0.5140 !!! WARNING: SEP 203 has a net charge of -0.4750 !!! WARNING: GLM 205 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6342645 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): -13.16100 42.96700 ymin,ymax (A): -21.65700 26.43900 zmin,zma (A): -5.804000 40.11700 x,y,z range (A): 56.12800 48.09600 45.92100 scale (grids/A): 0.6342645 object centre (A): 14.90300 2.390999 17.15650 number of atom coordinates read : 2734 total number of charged atoms : 2367 net assigned charge : 7.945013 assigned positive charge : 381.9251 centred at (gu) : 89.83298 88.34859 89.23587 assigned negative charge : -373.9807 centred at (gu) : 89.83899 88.29637 89.43187 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6613 nv = 96 ne = 84 npr = 51461 no. pairs analyzed = 51461 no. exposed pairs = 2905 no. arc points = 20232 no. surface atoms = 993 nbur = 1741 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3787 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1971 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7932 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3131162E-08 -7.9182598E-09 midg,1,midg; midg,igrid,midg 6.4903154E-09 1.0379081E-08 1,midg,midg; igrid,midg,midg 1.0654669E-08 8.8289474E-09 gauss-seidel spectral radius is 0.9871082 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 07:40:10 rms-change max change #iterations 0.1378055 22.17230 at 10iterations 1.3796125E-02 1.920906 at 20iterations 1.4998534E-03 0.2212200 at 30iterations 1.8893751E-04 3.0548096E-02 at 40iterations 2.8788958E-05 4.1580200E-03 at 50iterations finished qdiffx linear iterations at : 07:40:12 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 2.8788958E-05 4.1580200E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 07:40:13 3.116u 0.129s 0:03.54 91.2% 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 Tue Oct 11 2011 at 07:40:13 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIQ 56 has a net charge of 0.5140 !!! WARNING: SEP 203 has a net charge of -0.4750 !!! WARNING: GLM 205 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.902794 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): -13.16100 42.96700 ymin,ymax (A): -21.65700 26.43900 zmin,zma (A): -5.804000 40.11700 x,y,z range (A): 56.12800 48.09600 45.92100 scale (grids/A): 1.902794 object centre (A): 14.90300 2.390999 17.15650 number of atom coordinates read : 2734 total number of charged atoms : 2367 net assigned charge : 7.945013 assigned positive charge : 381.9251 centred at (gu) : 89.49841 85.04567 87.70743 assigned negative charge : -373.9807 centred at (gu) : 89.51671 84.88897 88.29543 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20232 grid for indexing accessible points = 1.400000 m= 25996 mr = 50698 m= 3966 mr = 19596 m= 203 mr = 2456 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 426 time to turn everything in is 0.5600000 number of dielectric boundary points 28900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18545 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) : 0.6342645 object centre at (A) : 14.90300 2.390999 17.15650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6052855E-02 -8.4441369E-03 midg,1,midg; midg,igrid,midg 5.8099655E-03 2.0316647E-02 1,midg,midg; igrid,midg,midg 2.0894397E-02 2.5788918E-02 gauss-seidel spectral radius is 0.9986128 estimated iterations to convergence 213 setup time was (sec) 0.8600000 now iterating at: 07:40:14 rms-change max change #iterations 4.125811 156.6122 at 10iterations 1.921838 65.46833 at 20iterations 0.8987427 32.94475 at 30iterations 0.4197402 13.60917 at 40iterations 0.1958373 5.866243 at 50iterations 9.1483034E-02 3.042999 at 60iterations 4.2594906E-02 1.375885 at 70iterations 1.9893508E-02 0.6364689 at 80iterations 9.3027484E-03 0.3070812 at 90iterations 4.3555764E-03 0.1386423 at 100iterations 2.0449003E-03 7.6049805E-02 at 110iterations 9.6079102E-04 3.4988403E-02 at 120iterations finished qdiffx linear iterations at : 07:40:20 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 9.6079102E-04 3.4988403E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 07:40:20 7.114u 0.181s 0:07.75 94.0% 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 Tue Oct 11 2011 at 07:40:20 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: 354 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2734 !!! WARNING: HIQ 56 has a net charge of 0.5140 !!! WARNING: SEP 203 has a net charge of -0.4750 !!! WARNING: GLM 205 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.854191 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): -13.16100 42.96700 ymin,ymax (A): -21.65700 26.43900 zmin,zma (A): -5.804000 40.11700 x,y,z range (A): 56.12800 48.09600 45.92100 scale (grids/A): 2.854191 object centre (A): 14.90300 2.390999 17.15650 number of atom coordinates read : 2734 total number of charged atoms : 2367 net assigned charge : 7.945013 assigned positive charge : 381.9251 centred at (gu) : 89.24761 82.56836 86.56104 assigned negative charge : -373.9807 centred at (gu) : 89.27523 82.33344 87.44313 start vw surface at 0.2100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 165596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20232 grid for indexing accessible points = 1.400000 m= 84969 mr = 122702 m= 30238 mr = 70698 m= 6959 mr = 24368 m= 1001 mr = 5248 m= 45 mr = 673 m= 2 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1272 time to turn everything in is 1.290000 number of dielectric boundary points 65116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 18934 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) : 1.902794 object centre at (A) : 14.90300 2.390999 17.15650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4524395 -0.1527593 midg,1,midg; midg,igrid,midg 2.9751454E-02 0.2058372 1,midg,midg; igrid,midg,midg 0.1159673 0.1797128 gauss-seidel spectral radius is 0.9992396 estimated iterations to convergence 286 setup time was (sec) 1.550000 now iterating at: 07:40:22 rms-change max change #iterations 9.640346 398.1993 at 10iterations 5.538413 112.3769 at 20iterations 3.172299 60.18272 at 30iterations 1.816553 36.51226 at 40iterations 1.037048 19.33142 at 50iterations 0.5913793 10.43146 at 60iterations 0.3380707 5.982982 at 70iterations 0.1929014 3.664555 at 80iterations 0.1098785 2.094713 at 90iterations 6.2942207E-02 1.115702 at 100iterations 3.5923436E-02 0.6588082 at 110iterations 2.0513020E-02 0.3899536 at 120iterations 1.1745005E-02 0.2341290 at 130iterations 6.7434297E-03 0.1303402 at 140iterations 3.8958129E-03 7.6624870E-02 at 150iterations 2.2774483E-03 4.3972015E-02 at 160iterations 1.3491422E-03 2.4776459E-02 at 170iterations 8.1770343E-04 1.5792847E-02 at 180iterations finished qdiffx linear iterations at : 07:40:34 total time elapsed so far: 13.24000 # loops : 180 mean,max change (kT/e) : 8.1770343E-04 1.5792847E-02 energy calculations done at 13.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 07:40:34 13.454u 0.214s 0:14.01 97.5% 0+0k 0+0io 0pf+0w