Wed Feb 8 12:12:24 PST 2012 #!/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 Feb 8 2012 at 12:12:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5392305 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 0.5392305 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.22553 90.96852 89.71351 assigned negative charge : -727.2772 centred at (gu) : 90.21529 90.93708 89.74884 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8844 nv = 96 ne = 84 npr = 99241 no. pairs analyzed = 99241 no. exposed pairs = 5806 no. arc points = 38942 no. surface atoms = 1955 nbur = 2848 mkacc time = 0.2000000 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 = 1.596000 m= 328 mr = 4858 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 4300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3879 ## 470 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 11748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6294128E-10 -3.2604938E-10 midg,1,midg; midg,igrid,midg -2.4887092E-10 2.7209737E-10 1,midg,midg; igrid,midg,midg -1.3058504E-10 3.6494620E-11 gauss-seidel spectral radius is 0.9824002 estimated iterations to convergence 62 setup time was (sec) 0.5900000 now iterating at: 12:12:25 rms-change max change #iterations 8.7223761E-02 12.01458 at 10iterations 6.0501006E-03 1.003487 at 20iterations 8.2578132E-04 0.1295223 at 30iterations 3.1698591E-04 4.0342331E-02 at 40iterations 1.4473058E-04 1.7981529E-02 at 50iterations finished qdiffx linear iterations at : 12:12:28 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 1.4473058E-04 1.7981529E-02 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 12:12:29 3.725u 0.180s 0:04.34 89.8% 0+0k 0+46544io 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 Feb 8 2012 at 12:12:29 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.617692 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 1.617692 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 90.67482 92.90411 89.13883 assigned negative charge : -727.2772 centred at (gu) : 90.64532 92.81075 89.24642 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 99745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38942 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31766 mr = 71074 m= 3322 mr = 22133 m= 88 mr = 1611 m= 0 mr = 9 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 860 time to turn everything in is 0.6200000 number of dielectric boundary points 40094 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 419 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 35502 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) : 0.5392305 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7462626E-03 7.3793177E-03 midg,1,midg; midg,igrid,midg -6.3532642E-03 -1.0245026E-02 1,midg,midg; igrid,midg,midg -3.3799414E-02 9.0885436E-04 gauss-seidel spectral radius is 0.9983255 estimated iterations to convergence 194 setup time was (sec) 0.8200000 now iterating at: 12:12:30 rms-change max change #iterations 4.295753 162.0122 at 10iterations 1.857688 63.20036 at 20iterations 0.8015866 24.50141 at 30iterations 0.3462918 11.54413 at 40iterations 0.1496928 4.339268 at 50iterations 6.4981095E-02 2.039022 at 60iterations 2.8191937E-02 0.8929424 at 70iterations 1.2294094E-02 0.3749494 at 80iterations 5.4482045E-03 0.1620359 at 90iterations 2.5109563E-03 7.4371338E-02 at 100iterations 1.2548373E-03 4.0961146E-02 at 110iterations 7.3255732E-04 2.2148132E-02 at 120iterations finished qdiffx linear iterations at : 12:12:37 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 7.3255732E-04 2.2148132E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 12:12:38 8.305u 0.206s 0:08.88 95.7% 0+0k 0+45600io 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 Feb 8 2012 at 12:12:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4803 !!! WARNING: HIZ 293 has a net charge of 0.2000 !!! WARNING: HIZ 297 has a net charge of 0.2000 !!! WARNING: GLM 316 has a net charge of -0.8000 !!! WARNING: ASP 608 has a net charge of -2.0000 !!! WARNING: ZN1 901 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.426537 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): -19.41100 46.60900 ymin,ymax (A): 8.106000 73.11600 zmin,zma (A): 33.70100 95.40100 x,y,z range (A): 66.02000 65.00999 61.70000 scale (grids/A): 2.426537 object centre (A): 13.59900 40.61100 64.55100 number of atom coordinates read : 4803 total number of charged atoms : 4644 net assigned charge : -0.9999646 assigned positive charge : 726.2723 centred at (gu) : 91.01172 94.35580 88.70792 assigned negative charge : -727.2772 centred at (gu) : 90.96791 94.21600 88.86935 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 232388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38942 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 109841 mr = 173741 m= 31828 mr = 87845 m= 5066 mr = 23958 m= 356 mr = 3235 m= 8 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2883 time to turn everything in is 1.570000 number of dielectric boundary points 90543 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 37112 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) : 1.617692 object centre at (A) : 13.59900 40.61100 64.55100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4217176E-02 0.1173075 midg,1,midg; midg,igrid,midg -0.1422417 -0.1439959 1,midg,midg; igrid,midg,midg -0.7308601 3.0534938E-02 gauss-seidel spectral radius is 0.9992195 estimated iterations to convergence 283 setup time was (sec) 1.810000 now iterating at: 12:12:40 rms-change max change #iterations 11.21527 281.1148 at 10iterations 6.556012 146.3300 at 20iterations 3.813161 82.60561 at 30iterations 2.204854 44.50260 at 40iterations 1.268940 24.12477 at 50iterations 0.7305850 14.03329 at 60iterations 0.4187451 7.818599 at 70iterations 0.2391161 4.299583 at 80iterations 0.1365785 2.902721 at 90iterations 7.8103103E-02 1.343113 at 100iterations 4.4547774E-02 0.8545487 at 110iterations 2.5335714E-02 0.4277658 at 120iterations 1.4467405E-02 0.2348728 at 130iterations 8.2884086E-03 0.1387522 at 140iterations 4.7901045E-03 7.8948975E-02 at 150iterations 2.8125350E-03 5.1071167E-02 at 160iterations 1.7030830E-03 3.2825232E-02 at 170iterations 1.0866584E-03 1.9191742E-02 at 180iterations finished qdiffx linear iterations at : 12:12:52 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 1.0866584E-03 1.9191742E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.66000 DelPhi exited at 12:12:52 13.670u 0.213s 0:14.23 97.5% 0+0k 0+45592io 0pf+0w