Sat Oct 15 14:14:01 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 Sat Oct 15 2011 at 14:14:01 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4645 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5236217 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): -24.24400 39.76500 ymin,ymax (A): -21.27200 45.84500 zmin,zma (A): 6.699000 74.68700 x,y,z range (A): 64.00900 67.11700 67.98801 scale (grids/A): 0.5236217 object centre (A): 7.760502 12.28650 40.69300 number of atom coordinates read : 4645 total number of charged atoms : 4405 net assigned charge : 8.300026 assigned positive charge : 702.0824 centred at (gu) : 91.20277 89.85491 87.86737 assigned negative charge : -693.7865 centred at (gu) : 91.32491 89.98573 87.75171 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8192 nv = 96 ne = 84 npr = 92713 no. pairs analyzed = 92713 no. exposed pairs = 6223 no. arc points = 42835 no. surface atoms = 2081 nbur = 2564 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 = 1.624000 m= 360 mr = 4127 m= 0 mr = 14 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4111 ## 543 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10665 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.0154680E-10 4.1527604E-10 midg,1,midg; midg,igrid,midg 8.0778800E-10 -3.3363151E-10 1,midg,midg; igrid,midg,midg 5.4516558E-10 -4.2750212E-10 gauss-seidel spectral radius is 0.9813408 estimated iterations to convergence 60 setup time was (sec) 0.5100000 now iterating at: 14:14:02 rms-change max change #iterations 7.5624324E-02 13.01819 at 10iterations 4.9237432E-03 0.8485565 at 20iterations 7.2013016E-04 9.1842651E-02 at 30iterations 2.2612743E-04 2.7556419E-02 at 40iterations 7.7550110E-05 9.8967552E-03 at 50iterations finished qdiffx linear iterations at : 14:14:08 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 7.7550110E-05 9.8967552E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 14:14:08 3.674u 0.192s 0:06.91 55.8% 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 15 2011 at 14:14:08 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4645 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.570865 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): -24.24400 39.76500 ymin,ymax (A): -21.27200 45.84500 zmin,zma (A): 6.699000 74.68700 x,y,z range (A): 64.00900 67.11700 67.98801 scale (grids/A): 1.570865 object centre (A): 7.760502 12.28650 40.69300 number of atom coordinates read : 4645 total number of charged atoms : 4405 net assigned charge : 8.300026 assigned positive charge : 702.0824 centred at (gu) : 93.60703 89.56316 83.60027 assigned negative charge : -693.7865 centred at (gu) : 93.97460 89.95686 83.25478 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 90642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42835 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 28578 mr = 60617 m= 3030 mr = 19413 m= 66 mr = 1358 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 40926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 463 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 33380 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) : 0.5236217 object centre at (A) : 7.760502 12.28650 40.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8941274E-03 2.1079293E-02 midg,1,midg; midg,igrid,midg 1.1607670E-02 -1.3963271E-02 1,midg,midg; igrid,midg,midg 1.3939589E-02 1.1271630E-05 gauss-seidel spectral radius is 0.9982117 estimated iterations to convergence 188 setup time was (sec) 0.7000000 now iterating at: 14:14:09 rms-change max change #iterations 3.972710 173.7131 at 10iterations 1.668586 55.87955 at 20iterations 0.6982769 23.36909 at 30iterations 0.2937024 9.823421 at 40iterations 0.1233961 3.924306 at 50iterations 5.1909070E-02 1.596292 at 60iterations 2.1866314E-02 0.6905251 at 70iterations 9.2754308E-03 0.3009796 at 80iterations 3.9684442E-03 0.1263042 at 90iterations 1.7321883E-03 5.9623718E-02 at 100iterations 8.0628507E-04 2.6679158E-02 at 110iterations 4.1285084E-04 1.2222290E-02 at 120iterations finished qdiffx linear iterations at : 14:14:17 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 4.1285084E-04 1.2222290E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 14:14:18 8.389u 0.206s 0:09.40 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 Sat Oct 15 2011 at 14:14:18 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4645 !!! WARNING: HEM 808 has a net charge of 1.4000 !!! WARNING: FE 3 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.356298 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): -24.24400 39.76500 ymin,ymax (A): -21.27200 45.84500 zmin,zma (A): 6.699000 74.68700 x,y,z range (A): 64.00900 67.11700 67.98801 scale (grids/A): 2.356298 object centre (A): 7.760502 12.28650 40.69300 number of atom coordinates read : 4645 total number of charged atoms : 4405 net assigned charge : 8.300026 assigned positive charge : 702.0824 centred at (gu) : 95.40997 89.34428 80.40018 assigned negative charge : -693.7865 centred at (gu) : 95.96180 89.93508 79.88201 start vw surface at 0.1200000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 210551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42835 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 97842 mr = 148623 m= 28453 mr = 76304 m= 4419 mr = 21223 m= 241 mr = 2789 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 92493 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 35169 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) : 1.570865 object centre at (A) : 7.760502 12.28650 40.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3925357 0.4578369 midg,1,midg; midg,igrid,midg 0.1556558 -0.2734559 1,midg,midg; igrid,midg,midg 0.2261433 3.2118253E-02 gauss-seidel spectral radius is 0.9991931 estimated iterations to convergence 278 setup time was (sec) 1.370000 now iterating at: 14:14:20 rms-change max change #iterations 10.60636 270.4516 at 10iterations 6.168467 155.4223 at 20iterations 3.552957 72.40748 at 30iterations 2.030965 43.64634 at 40iterations 1.158897 25.50121 at 50iterations 0.6584065 13.28590 at 60iterations 0.3735418 8.316089 at 70iterations 0.2115345 4.091955 at 80iterations 0.1193273 2.428542 at 90iterations 6.7378178E-02 1.420731 at 100iterations 3.7995923E-02 0.7113647 at 110iterations 2.1374848E-02 0.4412384 at 120iterations 1.2051008E-02 0.2358284 at 130iterations 6.7721289E-03 0.1292033 at 140iterations 3.8084325E-03 6.8162918E-02 at 150iterations 2.1442380E-03 4.2134285E-02 at 160iterations 1.2058818E-03 2.1836281E-02 at 170iterations 6.8143313E-04 1.3110161E-02 at 180iterations finished qdiffx linear iterations at : 14:14:44 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 6.8143313E-04 1.3110161E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 14:14:45 13.777u 0.253s 0:27.64 50.7% 0+0k 0+0io 0pf+0w