Mon Oct 10 17:01:11 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 Mon Oct 10 2011 at 17:01:12 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4394 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5146293 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): -16.52800 36.83400 ymin,ymax (A): -33.06800 31.43700 zmin,zma (A): -3.815000 65.36100 x,y,z range (A): 53.36200 64.50500 69.17600 scale (grids/A): 0.5146293 object centre (A): 10.15300 -0.8155003 30.77300 number of atom coordinates read : 4394 total number of charged atoms : 4150 net assigned charge : 3.700025 assigned positive charge : 654.8551 centred at (gu) : 90.29924 91.10173 87.57687 assigned negative charge : -651.1592 centred at (gu) : 90.15762 91.13904 87.59651 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7321 nv = 96 ne = 84 npr = 89770 no. pairs analyzed = 89770 no. exposed pairs = 5674 no. arc points = 39253 no. surface atoms = 1890 nbur = 2504 mkacc time = 0.1500000 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 = 1.652000 m= 274 mr = 3718 m= 0 mr = 10 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3724 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 9732 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1841320E-10 4.2029379E-12 midg,1,midg; midg,igrid,midg 1.2332342E-10 -5.9215161E-11 1,midg,midg; igrid,midg,midg -3.1406927E-10 4.8412785E-10 gauss-seidel spectral radius is 0.9806609 estimated iterations to convergence 59 setup time was (sec) 0.4900000 now iterating at: 17:01:12 rms-change max change #iterations 6.8778396E-02 12.69460 at 10iterations 4.1607525E-03 0.6558762 at 20iterations 5.2969524E-04 7.2800636E-02 at 30iterations 1.7720927E-04 2.2569895E-02 at 40iterations 6.5315973E-05 9.0166330E-03 at 50iterations finished qdiffx linear iterations at : 17:01:15 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 6.5315973E-05 9.0166330E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 17:01:16 3.521u 0.214s 0:04.65 80.2% 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 Mon Oct 10 2011 at 17:01:16 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4394 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.543888 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): -16.52800 36.83400 ymin,ymax (A): -33.06800 31.43700 zmin,zma (A): -3.815000 65.36100 x,y,z range (A): 53.36200 64.50500 69.17600 scale (grids/A): 1.543888 object centre (A): 10.15300 -0.8155003 30.77300 number of atom coordinates read : 4394 total number of charged atoms : 4150 net assigned charge : 3.700025 assigned positive charge : 654.8551 centred at (gu) : 90.89627 93.30410 82.72928 assigned negative charge : -651.1592 centred at (gu) : 90.47282 93.41684 82.78916 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 82974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23733 mr = 56495 m= 1978 mr = 15363 m= 39 mr = 768 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 36094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 509 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 31271 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) : 0.5146293 object centre at (A) : 10.15300 -0.8155003 30.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8902356E-03 8.6860973E-03 midg,1,midg; midg,igrid,midg -1.0362918E-03 -1.2381207E-02 1,midg,midg; igrid,midg,midg -4.6426891E-03 9.9002430E-03 gauss-seidel spectral radius is 0.9981062 estimated iterations to convergence 183 setup time was (sec) 0.6300000 now iterating at: 17:01:17 rms-change max change #iterations 3.663262 149.8774 at 10iterations 1.491815 52.70700 at 20iterations 0.6107684 21.60577 at 30iterations 0.2500823 8.798386 at 40iterations 0.1024241 3.908016 at 50iterations 4.2073522E-02 1.329697 at 60iterations 1.7187769E-02 0.5607808 at 70iterations 7.0739440E-03 0.2386026 at 80iterations 2.9202849E-03 0.1042743 at 90iterations 1.2214541E-03 4.2984486E-02 at 100iterations 5.2562868E-04 1.7814636E-02 at 110iterations 2.4319407E-04 7.7505112E-03 at 120iterations finished qdiffx linear iterations at : 17:01:24 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 2.4319407E-04 7.7505112E-03 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 17:01:25 8.000u 0.243s 0:09.07 90.8% 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 Mon Oct 10 2011 at 17:01:25 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4394 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.315832 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): -16.52800 36.83400 ymin,ymax (A): -33.06800 31.43700 zmin,zma (A): -3.815000 65.36100 x,y,z range (A): 53.36200 64.50500 69.17600 scale (grids/A): 2.315832 object centre (A): 10.15300 -0.8155003 30.77300 number of atom coordinates read : 4394 total number of charged atoms : 4150 net assigned charge : 3.700025 assigned positive charge : 654.8551 centred at (gu) : 91.34405 94.95588 79.09361 assigned negative charge : -651.1592 centred at (gu) : 90.70915 95.12521 79.18372 start vw surface at 0.1400000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 193495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 85037 mr = 139083 m= 20639 mr = 65696 m= 2833 mr = 14365 m= 164 mr = 1595 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 81362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 33084 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) : 1.543888 object centre at (A) : 10.15300 -0.8155003 30.77300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1521261 0.2495489 midg,1,midg; midg,igrid,midg -6.3969433E-02 -0.3123987 1,midg,midg; igrid,midg,midg -6.4086199E-02 0.1341465 gauss-seidel spectral radius is 0.9991525 estimated iterations to convergence 271 setup time was (sec) 1.270000 now iterating at: 17:01:27 rms-change max change #iterations 9.955875 254.7912 at 10iterations 5.684374 132.4518 at 20iterations 3.220213 72.42979 at 30iterations 1.816179 44.65322 at 40iterations 1.022837 21.59947 at 50iterations 0.5722739 12.51472 at 60iterations 0.3195204 7.181530 at 70iterations 0.1777719 3.687144 at 80iterations 9.9110968E-02 2.017111 at 90iterations 5.4989032E-02 1.143940 at 100iterations 3.0560501E-02 0.5954742 at 110iterations 1.6964952E-02 0.3498764 at 120iterations 9.4078993E-03 0.1832342 at 130iterations 5.2113933E-03 0.1050682 at 140iterations 2.8867554E-03 5.8908463E-02 at 150iterations 1.6056077E-03 3.7048340E-02 at 160iterations 8.9015980E-04 1.7456055E-02 at 170iterations 4.9623224E-04 9.4480515E-03 at 180iterations finished qdiffx linear iterations at : 17:01:39 total time elapsed so far: 12.91000 # loops : 180 mean,max change (kT/e) : 4.9623224E-04 9.4480515E-03 energy calculations done at 12.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 17:01:40 13.043u 0.207s 0:14.49 91.3% 0+0k 0+0io 0pf+0w