Wed Dec 21 14:20:44 PST 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 Wed Dec 21 2011 at 14:20:44 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6497180 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): -5.354000 33.90200 ymin,ymax (A): -3.317000 46.65500 zmin,zma (A): -7.936000 46.85700 x,y,z range (A): 39.25600 49.97200 54.79300 scale (grids/A): 0.6497180 object centre (A): 14.27400 21.66900 19.46050 number of atom coordinates read : 1958 total number of charged atoms : 1762 net assigned charge : -18.57600 assigned positive charge : 264.3865 centred at (gu) : 89.48572 92.95370 89.87951 assigned negative charge : -282.9623 centred at (gu) : 89.42722 93.05216 89.94290 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5601 nv = 96 ne = 84 npr = 40903 no. pairs analyzed = 40903 no. exposed pairs = 2465 no. arc points = 17196 no. surface atoms = 837 nbur = 1121 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3156 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.1600000 number of dielectric boundary points 2708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1563 ## 106 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8671881E-08 -4.0809685E-08 midg,1,midg; midg,igrid,midg -1.3618474E-08 -8.5035751E-08 1,midg,midg; igrid,midg,midg -4.5899913E-08 -2.5726967E-08 gauss-seidel spectral radius is 0.9876653 estimated iterations to convergence 74 setup time was (sec) 0.3500000 now iterating at: 14:20:44 rms-change max change #iterations 0.1326777 21.44106 at 10iterations 1.3484158E-02 2.193220 at 20iterations 1.3882488E-03 0.2122574 at 30iterations 1.4513356E-04 2.2886276E-02 at 40iterations 1.4692288E-05 2.0446777E-03 at 50iterations finished qdiffx linear iterations at : 14:20:47 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.4692288E-05 2.0446777E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 14:20:48 3.370u 0.180s 0:04.41 80.4% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:20:48 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.949154 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): -5.354000 33.90200 ymin,ymax (A): -3.317000 46.65500 zmin,zma (A): -7.936000 46.85700 x,y,z range (A): 39.25600 49.97200 54.79300 scale (grids/A): 1.949154 object centre (A): 14.27400 21.66900 19.46050 number of atom coordinates read : 1958 total number of charged atoms : 1762 net assigned charge : -18.57600 assigned positive charge : 264.3865 centred at (gu) : 88.45751 98.86143 89.63873 assigned negative charge : -282.9623 centred at (gu) : 88.28193 99.15675 89.82876 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 60591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 21159 mr = 41995 m= 2834 mr = 15896 m= 145 mr = 1724 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 649 time to turn everything in is 0.3200000 number of dielectric boundary points 25072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 13800 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) : 0.6497180 object centre at (A) : 14.27400 21.66900 19.46050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4299962E-02 7.6532271E-03 midg,1,midg; midg,igrid,midg -1.1275733E-02 -0.1030961 1,midg,midg; igrid,midg,midg -2.9597653E-02 -1.9226504E-02 gauss-seidel spectral radius is 0.9986142 estimated iterations to convergence 213 setup time was (sec) 0.5300000 now iterating at: 14:20:49 rms-change max change #iterations 3.695420 199.6940 at 10iterations 1.722211 72.91940 at 20iterations 0.7999250 29.85926 at 30iterations 0.3737564 13.41081 at 40iterations 0.1729988 6.229252 at 50iterations 8.0457181E-02 2.936403 at 60iterations 3.7689362E-02 1.360608 at 70iterations 1.7513350E-02 0.6710091 at 80iterations 8.1632761E-03 0.3017870 at 90iterations 3.7975863E-03 0.1377331 at 100iterations 1.7618834E-03 6.7785263E-02 at 110iterations 8.2208094E-04 3.6336899E-02 at 120iterations finished qdiffx linear iterations at : 14:20:56 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 8.2208094E-04 3.6336899E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 14:20:57 8.036u 0.207s 0:08.62 95.4% 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 Wed Dec 21 2011 at 14:20:57 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: 232 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.923731 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): -5.354000 33.90200 ymin,ymax (A): -3.317000 46.65500 zmin,zma (A): -7.936000 46.85700 x,y,z range (A): 39.25600 49.97200 54.79300 scale (grids/A): 2.923731 object centre (A): 14.27400 21.66900 19.46050 number of atom coordinates read : 1958 total number of charged atoms : 1762 net assigned charge : -18.57600 assigned positive charge : 264.3865 centred at (gu) : 87.68641 103.2922 89.45815 assigned negative charge : -282.9623 centred at (gu) : 87.42297 103.7351 89.74315 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 139952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 69860 mr = 101290 m= 23504 mr = 57897 m= 4935 mr = 19130 m= 610 mr = 3642 m= 43 mr = 390 m= 0 mr = 22 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2331 time to turn everything in is 0.7800000 number of dielectric boundary points 56533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 14087 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) : 1.949154 object centre at (A) : 14.27400 21.66900 19.46050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6463432 0.7120351 midg,1,midg; midg,igrid,midg -3.3854328E-02 -1.059854 1,midg,midg; igrid,midg,midg -0.2368743 -0.1791123 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 1.010000 now iterating at: 14:20:58 rms-change max change #iterations 8.585374 414.6882 at 10iterations 4.968363 157.5756 at 20iterations 2.849844 69.91339 at 30iterations 1.631947 37.97276 at 40iterations 0.9358266 29.60807 at 50iterations 0.5354483 12.48911 at 60iterations 0.3052849 6.647215 at 70iterations 0.1740658 3.667718 at 80iterations 9.9198617E-02 1.992840 at 90iterations 5.6627382E-02 1.447891 at 100iterations 3.2234561E-02 0.6503661 at 110iterations 1.8403595E-02 0.3637352 at 120iterations 1.0498771E-02 0.2109642 at 130iterations 5.9696287E-03 0.1314192 at 140iterations 3.3993446E-03 6.9028854E-02 at 150iterations 1.9404063E-03 3.9737701E-02 at 160iterations 1.1031234E-03 2.0357132E-02 at 170iterations 6.2975392E-04 1.3086319E-02 at 180iterations finished qdiffx linear iterations at : 14:21:10 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 6.2975392E-04 1.3086319E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 14:21:10 12.907u 0.299s 0:13.57 97.1% 0+0k 0+0io 0pf+0w