Mon Oct 10 09:44:04 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 09:44:04 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 = 2737 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: 0.5796441 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): -17.64700 34.03300 ymin,ymax (A): -59.83700 -0.9110001 zmin,zma (A): -0.5100000 60.90700 x,y,z range (A): 51.68000 58.92600 61.41700 scale (grids/A): 0.5796441 object centre (A): 8.192999 -30.37400 30.19850 number of atom coordinates read : 2737 total number of charged atoms : 2590 net assigned charge : 8.000017 assigned positive charge : 398.8362 centred at (gu) : 88.01591 88.01702 88.00789 assigned negative charge : -390.8365 centred at (gu) : 88.04080 87.88734 87.93960 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6319 nv = 96 ne = 84 npr = 51912 no. pairs analyzed = 51912 no. exposed pairs = 4176 no. arc points = 30741 no. surface atoms = 1387 nbur = 1350 mkacc time = 9.0000004E-02 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 = 1.484000 m= 330 mr = 2720 m= 4 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7838 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1188244E-10 1.9340523E-09 midg,1,midg; midg,igrid,midg -1.2009091E-09 2.6461369E-09 1,midg,midg; igrid,midg,midg 3.5585044E-09 8.4359647E-10 gauss-seidel spectral radius is 0.9846421 estimated iterations to convergence 66 setup time was (sec) 0.3800000 now iterating at: 09:44:05 rms-change max change #iterations 9.2397295E-02 14.95806 at 10iterations 7.0870807E-03 0.9937859 at 20iterations 5.6430383E-04 8.9902878E-02 at 30iterations 5.2702930E-05 8.1930161E-03 at 40iterations 7.8135681E-06 1.0604858E-03 at 50iterations finished qdiffx linear iterations at : 09:44:08 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 7.8135681E-06 1.0604858E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 09:44:08 3.352u 0.183s 0:03.87 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 Mon Oct 10 2011 at 09:44:08 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 = 2737 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: 1.738932 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): -17.64700 34.03300 ymin,ymax (A): -59.83700 -0.9110001 zmin,zma (A): -0.5100000 60.90700 x,y,z range (A): 51.68000 58.92600 61.41700 scale (grids/A): 1.738932 object centre (A): 8.192999 -30.37400 30.19850 number of atom coordinates read : 2737 total number of charged atoms : 2590 net assigned charge : 8.000017 assigned positive charge : 398.8362 centred at (gu) : 84.04724 84.05061 84.02306 assigned negative charge : -390.8365 centred at (gu) : 84.12232 83.66187 83.81857 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30741 grid for indexing accessible points = 1.400000 m= 20945 mr = 40406 m= 2864 mr = 13138 m= 139 mr = 1286 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 36457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20116 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) : 0.5796441 object centre at (A) : 8.192999 -30.37400 30.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9452732E-03 1.9089755E-03 midg,1,midg; midg,igrid,midg 3.0447943E-02 2.6832974E-02 1,midg,midg; igrid,midg,midg 1.1768369E-02 4.2007263E-03 gauss-seidel spectral radius is 0.9984092 estimated iterations to convergence 199 setup time was (sec) 0.5600000 now iterating at: 09:44:09 rms-change max change #iterations 3.593550 170.7703 at 10iterations 1.577114 64.52457 at 20iterations 0.6958457 29.92297 at 30iterations 0.3054674 12.38428 at 40iterations 0.1347028 4.782365 at 50iterations 5.9204184E-02 2.113611 at 60iterations 2.6061388E-02 1.038795 at 70iterations 1.1466536E-02 0.3961182 at 80iterations 5.0321268E-03 0.1786041 at 90iterations 2.2220779E-03 8.3129883E-02 at 100iterations 9.7960327E-04 3.5331726E-02 at 110iterations 4.3078666E-04 1.5292168E-02 at 120iterations finished qdiffx linear iterations at : 09:44:16 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 4.3078666E-04 1.5292168E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 09:44:16 7.723u 0.185s 0:08.19 96.4% 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 Mon Oct 10 2011 at 09:44:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 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: 2.608398 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): -17.64700 34.03300 ymin,ymax (A): -59.83700 -0.9110001 zmin,zma (A): -0.5100000 60.90700 x,y,z range (A): 51.68000 58.92600 61.41700 scale (grids/A): 2.608398 object centre (A): 8.192999 -30.37400 30.19850 number of atom coordinates read : 2737 total number of charged atoms : 2590 net assigned charge : 8.000017 assigned positive charge : 398.8362 centred at (gu) : 81.07073 81.07577 81.03451 assigned negative charge : -390.8365 centred at (gu) : 81.18336 80.49266 80.72775 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30741 grid for indexing accessible points = 1.400000 m= 68555 mr = 100144 m= 22254 mr = 50658 m= 4628 mr = 15651 m= 473 mr = 2795 m= 21 mr = 204 m= 0 mr = 1 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 82227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20712 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) : 1.738932 object centre at (A) : 8.192999 -30.37400 30.19850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1926052 -4.0193673E-02 midg,1,midg; midg,igrid,midg 0.5960871 0.3651471 1,midg,midg; igrid,midg,midg 5.2454289E-02 5.0344184E-02 gauss-seidel spectral radius is 0.9992239 estimated iterations to convergence 283 setup time was (sec) 1.070000 now iterating at: 09:44:18 rms-change max change #iterations 9.312016 299.8284 at 10iterations 5.533925 166.9231 at 20iterations 3.246170 83.44290 at 30iterations 1.884980 49.01900 at 40iterations 1.089816 31.60274 at 50iterations 0.6287686 17.51061 at 60iterations 0.3607470 9.181597 at 70iterations 0.2068434 4.760113 at 80iterations 0.1180552 2.653464 at 90iterations 6.7232549E-02 1.506994 at 100iterations 3.8242664E-02 0.9001114 at 110iterations 2.1818781E-02 0.4692230 at 120iterations 1.2391001E-02 0.2637405 at 130iterations 7.0401449E-03 0.1404285 at 140iterations 3.9961166E-03 9.0705872E-02 at 150iterations 2.2699495E-03 4.5829654E-02 at 160iterations 1.2872549E-03 2.5556564E-02 at 170iterations 7.2993198E-04 1.5163422E-02 at 180iterations finished qdiffx linear iterations at : 09:44:29 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 7.2993198E-04 1.5163422E-02 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 09:44:30 12.529u 0.206s 0:13.24 96.0% 0+0k 0+0io 0pf+0w