Sat Oct 8 18:12:31 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+sph2.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 = amb2.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 Sat Oct 8 2011 at 18:12:32 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3614 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: 0.5716488 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): -1.943000 60.33300 ymin,ymax (A): -19.73900 37.93300 zmin,zma (A): -5.426000 55.11000 x,y,z range (A): 62.27600 57.67200 60.53600 scale (grids/A): 0.5716488 object centre (A): 29.19500 9.097001 24.84200 number of atom coordinates read : 3614 total number of charged atoms : 3466 net assigned charge : -7.499979 assigned positive charge : 546.2260 centred at (gu) : 88.95686 88.06690 90.99899 assigned negative charge : -553.7278 centred at (gu) : 89.02263 88.08462 91.00353 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7803 nv = 96 ne = 84 npr = 72773 no. pairs analyzed = 72773 no. exposed pairs = 4609 no. arc points = 31902 no. surface atoms = 1550 nbur = 2064 mkacc time = 0.1600000 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 = 1.512000 m= 362 mr = 4170 m= 0 mr = 26 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3246 ## 365 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10007 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.0913632E-10 -1.6751932E-09 midg,1,midg; midg,igrid,midg -1.3528142E-09 -1.0257936E-09 1,midg,midg; igrid,midg,midg 1.5754606E-10 -2.0344106E-09 gauss-seidel spectral radius is 0.9842594 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 18:12:32 rms-change max change #iterations 0.1047576 14.75988 at 10iterations 8.0240406E-03 1.364647 at 20iterations 7.3145388E-04 0.1069622 at 30iterations 1.3301312E-04 2.5157928E-02 at 40iterations 3.7159782E-05 7.3285103E-03 at 50iterations finished qdiffx linear iterations at : 18:12:36 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 3.7159782E-05 7.3285103E-03 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.360000 DelPhi exited at 18:12:36 4.366u 0.258s 0:04.89 94.2% 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 Sat Oct 8 2011 at 18:12:36 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3614 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: 1.714946 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): -1.943000 60.33300 ymin,ymax (A): -19.73900 37.93300 zmin,zma (A): -5.426000 55.11000 x,y,z range (A): 62.27600 57.67200 60.53600 scale (grids/A): 1.714946 object centre (A): 29.19500 9.097001 24.84200 number of atom coordinates read : 3614 total number of charged atoms : 3466 net assigned charge : -7.499979 assigned positive charge : 546.2260 centred at (gu) : 86.86926 84.19979 92.99598 assigned negative charge : -553.7278 centred at (gu) : 87.06739 84.25360 93.01026 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85606 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31902 grid for indexing accessible points = 1.400000 m= 28557 mr = 59245 m= 3365 mr = 20045 m= 122 mr = 1750 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1323 time to turn everything in is 0.6500000 number of dielectric boundary points 36600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 26822 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) : 0.5716488 object centre at (A) : 29.19500 9.097001 24.84200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9368292E-03 -8.3937310E-03 midg,1,midg; midg,igrid,midg -1.5546378E-02 -3.6269494E-03 1,midg,midg; igrid,midg,midg -1.7768374E-02 -4.0001027E-02 gauss-seidel spectral radius is 0.9984213 estimated iterations to convergence 200 setup time was (sec) 0.9900000 now iterating at: 18:12:38 rms-change max change #iterations 4.213142 194.3101 at 10iterations 1.862014 65.88720 at 20iterations 0.8207050 24.58694 at 30iterations 0.3629415 11.73805 at 40iterations 0.1604809 5.149456 at 50iterations 7.1412265E-02 2.312233 at 60iterations 3.1506207E-02 0.9454088 at 70iterations 1.4056393E-02 0.4258327 at 80iterations 6.2208888E-03 0.2090225 at 90iterations 2.7682043E-03 0.1037822 at 100iterations 1.2399448E-03 4.0131092E-02 at 110iterations 5.6366157E-04 1.8352509E-02 at 120iterations finished qdiffx linear iterations at : 18:12:47 total time elapsed so far: 9.960000 # loops : 120 mean,max change (kT/e) : 5.6366157E-04 1.8352509E-02 energy calculations done at 9.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 18:12:47 10.147u 0.280s 0:10.70 97.3% 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 Sat Oct 8 2011 at 18:12:47 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3614 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: 2.572419 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): -1.943000 60.33300 ymin,ymax (A): -19.73900 37.93300 zmin,zma (A): -5.426000 55.11000 x,y,z range (A): 62.27600 57.67200 60.53600 scale (grids/A): 2.572419 object centre (A): 29.19500 9.097001 24.84200 number of atom coordinates read : 3614 total number of charged atoms : 3466 net assigned charge : -7.499979 assigned positive charge : 546.2260 centred at (gu) : 85.30354 81.29956 94.49371 assigned negative charge : -553.7278 centred at (gu) : 85.60098 81.38046 94.51521 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 198388 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31902 grid for indexing accessible points = 1.400000 m= 96497 mr = 143992 m= 29982 mr = 77410 m= 5577 mr = 22946 m= 465 mr = 3767 m= 12 mr = 214 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 4318 time to turn everything in is 1.630000 number of dielectric boundary points 82593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 27703 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) : 1.714946 object centre at (A) : 29.19500 9.097001 24.84200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8460295E-03 0.1694192 midg,1,midg; midg,igrid,midg -0.2109690 -4.9849011E-02 1,midg,midg; igrid,midg,midg -0.3541883 -0.6385350 gauss-seidel spectral radius is 0.9992226 estimated iterations to convergence 283 setup time was (sec) 2.010000 now iterating at: 18:12:50 rms-change max change #iterations 10.50399 303.8555 at 10iterations 6.083808 145.2165 at 20iterations 3.502284 77.01964 at 30iterations 2.005604 41.35230 at 40iterations 1.149331 26.50095 at 50iterations 0.6538563 11.85671 at 60iterations 0.3734926 6.941281 at 70iterations 0.2121804 3.977222 at 80iterations 0.1205711 2.282286 at 90iterations 6.8463668E-02 1.211008 at 100iterations 3.9005727E-02 0.6896534 at 110iterations 2.2090398E-02 0.3978977 at 120iterations 1.2528014E-02 0.2315822 at 130iterations 7.1126199E-03 0.1276016 at 140iterations 4.0443214E-03 7.2965622E-02 at 150iterations 2.3001176E-03 4.7859192E-02 at 160iterations 1.3117946E-03 2.3503304E-02 at 170iterations 7.5346598E-04 1.2184143E-02 at 180iterations finished qdiffx linear iterations at : 18:13:05 total time elapsed so far: 17.17000 # loops : 180 mean,max change (kT/e) : 7.5346598E-04 1.2184143E-02 energy calculations done at 17.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.36000 DelPhi exited at 18:13:05 17.359u 0.392s 0:18.04 98.3% 0+0k 0+0io 0pf+0w