Tue Oct 11 03:48:47 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 Tue Oct 11 2011 at 03:48:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 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: 0.6740126 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): -9.417000 36.74600 ymin,ymax (A): -27.43400 21.68500 zmin,zma (A): -7.296000 45.52200 x,y,z range (A): 46.16300 49.11900 52.81800 scale (grids/A): 0.6740126 object centre (A): 13.66450 -2.874500 19.11300 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 4.500013 assigned positive charge : 403.2438 centred at (gu) : 89.50903 90.42070 91.31618 assigned negative charge : -398.7444 centred at (gu) : 89.23864 90.25198 91.29435 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8136 nv = 96 ne = 84 npr = 55053 no. pairs analyzed = 55053 no. exposed pairs = 3223 no. arc points = 22209 no. surface atoms = 1087 nbur = 1586 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4696 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.4000000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2056690E-09 3.0124099E-08 midg,1,midg; midg,igrid,midg -2.9872599E-08 7.0471174E-08 1,midg,midg; igrid,midg,midg -7.0358539E-08 8.3743075E-08 gauss-seidel spectral radius is 0.9885905 estimated iterations to convergence 76 setup time was (sec) 0.7000000 now iterating at: 03:48:48 rms-change max change #iterations 0.1845355 24.81343 at 10iterations 2.0708721E-02 2.724468 at 20iterations 2.3685046E-03 0.3043213 at 30iterations 2.9092474E-04 3.6365509E-02 at 40iterations 4.4029388E-05 5.9547424E-03 at 50iterations finished qdiffx linear iterations at : 03:48:51 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 4.4029388E-05 5.9547424E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 03:48:52 4.121u 0.199s 0:04.72 91.3% 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 03:48:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 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: 2.022038 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): -9.417000 36.74600 ymin,ymax (A): -27.43400 21.68500 zmin,zma (A): -7.296000 45.52200 x,y,z range (A): 46.16300 49.11900 52.81800 scale (grids/A): 2.022038 object centre (A): 13.66450 -2.874500 19.11300 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 4.500013 assigned positive charge : 403.2438 centred at (gu) : 88.52676 91.26167 93.94798 assigned negative charge : -398.7444 centred at (gu) : 87.71584 90.75567 93.88273 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 87374 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 33808 mr = 62363 m= 5899 mr = 25783 m= 417 mr = 3972 m= 5 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.8200000 number of dielectric boundary points 35208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 19989 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) : 0.6740126 object centre at (A) : 13.66450 -2.874500 19.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2748495E-02 7.2720917E-03 midg,1,midg; midg,igrid,midg -1.0428848E-02 5.1915638E-02 1,midg,midg; igrid,midg,midg -3.5793819E-02 6.8620995E-02 gauss-seidel spectral radius is 0.9987851 estimated iterations to convergence 227 setup time was (sec) 1.180000 now iterating at: 03:48:54 rms-change max change #iterations 4.840683 195.4152 at 10iterations 2.372789 77.94748 at 20iterations 1.163218 34.68559 at 30iterations 0.5699007 16.47032 at 40iterations 0.2796957 8.353561 at 50iterations 0.1370316 3.973560 at 60iterations 6.6947341E-02 1.810139 at 70iterations 3.2918800E-02 1.069799 at 80iterations 1.6111452E-02 0.4716454 at 90iterations 7.9010427E-03 0.2186871 at 100iterations 3.8756740E-03 0.1067615 at 110iterations 1.9032295E-03 5.6888580E-02 at 120iterations finished qdiffx linear iterations at : 03:49:01 total time elapsed so far: 9.030000 # loops : 120 mean,max change (kT/e) : 1.9032295E-03 5.6888580E-02 energy calculations done at 9.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 03:49:02 9.271u 0.210s 0:09.98 94.9% 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 03:49:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2673 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: 3.033057 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): -9.417000 36.74600 ymin,ymax (A): -27.43400 21.68500 zmin,zma (A): -7.296000 45.52200 x,y,z range (A): 46.16300 49.11900 52.81800 scale (grids/A): 3.033057 object centre (A): 13.66450 -2.874500 19.11300 number of atom coordinates read : 2673 total number of charged atoms : 2526 net assigned charge : 4.500013 assigned positive charge : 403.2438 centred at (gu) : 87.78996 91.89233 95.92188 assigned negative charge : -398.7444 centred at (gu) : 86.57367 91.13363 95.82399 start vw surface at 0.1900000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 201625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 107343 mr = 150145 m= 41735 mr = 89616 m= 10893 mr = 34520 m= 1814 mr = 8521 m= 125 mr = 1297 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 856 time to turn everything in is 2.100000 number of dielectric boundary points 79383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 20206 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) : 2.022038 object centre at (A) : 13.66450 -2.874500 19.11300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9640069E-02 0.2633467 midg,1,midg; midg,igrid,midg -0.1150667 0.5389664 1,midg,midg; igrid,midg,midg -0.2780667 0.5631578 gauss-seidel spectral radius is 0.9992921 estimated iterations to convergence 297 setup time was (sec) 2.470000 now iterating at: 03:49:05 rms-change max change #iterations 10.98702 352.7659 at 10iterations 6.492179 134.8371 at 20iterations 3.809601 89.99834 at 30iterations 2.237335 44.83814 at 40iterations 1.313517 20.91846 at 50iterations 0.7694212 14.67134 at 60iterations 0.4501409 7.743198 at 70iterations 0.2631692 4.366816 at 80iterations 0.1539547 2.476913 at 90iterations 8.9890763E-02 1.497139 at 100iterations 5.2505270E-02 0.9410477 at 110iterations 3.0723421E-02 0.5316887 at 120iterations 1.7939132E-02 0.2953262 at 130iterations 1.0542288E-02 0.1935635 at 140iterations 6.1834236E-03 9.7431183E-02 at 150iterations 3.6525629E-03 6.4085007E-02 at 160iterations 2.1894011E-03 3.7341118E-02 at 170iterations 1.3323462E-03 2.5505066E-02 at 180iterations finished qdiffx linear iterations at : 03:49:17 total time elapsed so far: 14.83000 # loops : 180 mean,max change (kT/e) : 1.3323462E-03 2.5505066E-02 energy calculations done at 14.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.06000 DelPhi exited at 03:49:18 15.060u 0.235s 0:15.94 95.9% 0+0k 0+0io 0pf+0w