Wed Dec 28 11:03:19 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+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 Wed Dec 28 2011 at 11:03:19 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6020632 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): -8.849000 50.28100 ymin,ymax (A): 8.693001 51.78400 zmin,zma (A): -4.016000 38.87800 x,y,z range (A): 59.13000 43.09100 42.89400 scale (grids/A): 0.6020632 object centre (A): 20.71600 30.23850 17.43100 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 290.5560 centred at (gu) : 90.19238 89.03810 90.46191 assigned negative charge : -286.5562 centred at (gu) : 90.17085 88.92423 90.63182 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4809 nv = 96 ne = 84 npr = 39677 no. pairs analyzed = 39677 no. exposed pairs = 2441 no. arc points = 17113 no. surface atoms = 827 nbur = 1131 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 246 mr = 2663 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2700000 number of dielectric boundary points 2383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 5802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0127361E-09 -3.4315970E-09 midg,1,midg; midg,igrid,midg -1.7921294E-09 4.1240371E-09 1,midg,midg; igrid,midg,midg 1.2261225E-09 2.6228018E-09 gauss-seidel spectral radius is 0.9856675 estimated iterations to convergence 68 setup time was (sec) 0.7500000 now iterating at: 11:03:21 rms-change max change #iterations 9.8526284E-02 15.56464 at 10iterations 8.2251681E-03 1.382801 at 20iterations 7.0325896E-04 0.1461811 at 30iterations 5.8662245E-05 1.1409760E-02 at 40iterations 5.0109184E-06 8.7165833E-04 at 50iterations finished qdiffx linear iterations at : 11:03:27 total time elapsed so far: 6.970000 # loops : 50 mean,max change (kT/e) : 5.0109184E-06 8.7165833E-04 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 11:03:28 7.154u 0.790s 0:08.40 94.5% 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 28 2011 at 11:03:28 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.806190 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): -8.849000 50.28100 ymin,ymax (A): 8.693001 51.78400 zmin,zma (A): -4.016000 38.87800 x,y,z range (A): 59.13000 43.09100 42.89400 scale (grids/A): 1.806190 object centre (A): 20.71600 30.23850 17.43100 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 290.5560 centred at (gu) : 90.57738 87.11429 91.38590 assigned negative charge : -286.5562 centred at (gu) : 90.51273 86.77280 91.89556 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 52334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 18263 mr = 36021 m= 2298 mr = 13603 m= 68 mr = 1365 m= 0 mr = 9 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 233 time to turn everything in is 0.5100000 number of dielectric boundary points 21965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14280 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) : 0.6020632 object centre at (A) : 20.71600 30.23850 17.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5535431E-03 -3.4581302E-03 midg,1,midg; midg,igrid,midg 2.0148768E-03 7.5823572E-03 1,midg,midg; igrid,midg,midg 2.7399749E-02 4.2416438E-02 gauss-seidel spectral radius is 0.9984085 estimated iterations to convergence 199 setup time was (sec) 1.040000 now iterating at: 11:03:30 rms-change max change #iterations 3.217755 157.8681 at 10iterations 1.416522 63.05654 at 20iterations 0.6255926 26.53611 at 30iterations 0.2756725 10.37807 at 40iterations 0.1212546 4.514552 at 50iterations 5.3504281E-02 2.104420 at 60iterations 2.3563810E-02 0.8878474 at 70iterations 1.0332125E-02 0.3979480 at 80iterations 4.5680194E-03 0.1841111 at 90iterations 2.0134461E-03 8.2234383E-02 at 100iterations 8.8687940E-04 3.1795502E-02 at 110iterations 3.8963740E-04 1.4404297E-02 at 120iterations finished qdiffx linear iterations at : 11:03:46 total time elapsed so far: 17.80000 # loops : 120 mean,max change (kT/e) : 3.8963740E-04 1.4404297E-02 energy calculations done at 17.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 11:03:47 17.996u 0.807s 0:19.50 96.3% 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 Wed Dec 28 2011 at 11:03:47 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.709285 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): -8.849000 50.28100 ymin,ymax (A): 8.693001 51.78400 zmin,zma (A): -4.016000 38.87800 x,y,z range (A): 59.13000 43.09100 42.89400 scale (grids/A): 2.709285 object centre (A): 20.71600 30.23850 17.43100 number of atom coordinates read : 1958 total number of charged atoms : 1826 net assigned charge : 4.000004 assigned positive charge : 290.5560 centred at (gu) : 90.86604 85.67141 92.07887 assigned negative charge : -286.5562 centred at (gu) : 90.76905 85.15916 92.84340 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 121219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17113 grid for indexing accessible points = 1.400000 m= 60435 mr = 87108 m= 20236 mr = 49947 m= 3804 mr = 16493 m= 295 mr = 2820 m= 6 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 778 time to turn everything in is 1.290000 number of dielectric boundary points 49470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 14608 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) : 1.806190 object centre at (A) : 20.71600 30.23850 17.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2845414E-02 -7.8338794E-03 midg,1,midg; midg,igrid,midg 8.8833787E-02 6.1780717E-02 1,midg,midg; igrid,midg,midg 0.2991817 0.5789363 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.850000 now iterating at: 11:03:50 rms-change max change #iterations 7.846375 326.1647 at 10iterations 4.439553 122.0820 at 20iterations 2.489822 59.33701 at 30iterations 1.395689 33.51527 at 40iterations 0.7789627 18.61830 at 50iterations 0.4348548 10.14573 at 60iterations 0.2425865 5.695717 at 70iterations 0.1347431 2.992506 at 80iterations 7.5071305E-02 1.615694 at 90iterations 4.1839670E-02 0.9956055 at 100iterations 2.3311261E-02 0.5842419 at 110iterations 1.3005044E-02 0.3036008 at 120iterations 7.2118156E-03 0.1514912 at 130iterations 4.0203496E-03 8.5075378E-02 at 140iterations 2.2384638E-03 5.1551819E-02 at 150iterations 1.2451648E-03 2.4800777E-02 at 160iterations 6.9052126E-04 1.7205477E-02 at 170iterations 3.8587567E-04 8.6492300E-03 at 180iterations finished qdiffx linear iterations at : 11:04:17 total time elapsed so far: 28.96000 # loops : 180 mean,max change (kT/e) : 3.8587567E-04 8.6492300E-03 energy calculations done at 28.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.13000 DelPhi exited at 11:04:18 29.137u 0.907s 0:30.37 98.8% 0+0k 0+0io 0pf+0w