Tue Oct 11 08:33:53 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 08:33:53 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 = 2086 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: 0.7012291 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): -19.56200 26.14400 ymin,ymax (A): -12.58200 28.37800 zmin,zma (A): -2.379000 48.38900 x,y,z range (A): 45.70600 40.96000 50.76800 scale (grids/A): 0.7012291 object centre (A): 3.290999 7.898000 23.00500 number of atom coordinates read : 2086 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 89.24845 89.82719 90.04910 assigned negative charge : -312.6442 centred at (gu) : 89.14447 89.85483 90.10133 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6848 nv = 96 ne = 84 npr = 41528 no. pairs analyzed = 41528 no. exposed pairs = 2584 no. arc points = 17293 no. surface atoms = 876 nbur = 1210 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3911 m= 7 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1581 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7754 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9403804E-08 2.5280588E-08 midg,1,midg; midg,igrid,midg 6.1561309E-08 3.4618292E-08 1,midg,midg; igrid,midg,midg 2.3173010E-09 7.9506762E-08 gauss-seidel spectral radius is 0.9893992 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 08:33:54 rms-change max change #iterations 0.1946161 28.99991 at 10iterations 2.4033738E-02 3.767475 at 20iterations 3.1930197E-03 0.4170387 at 30iterations 5.5457966E-04 7.6675415E-02 at 40iterations 1.4943554E-04 1.8352509E-02 at 50iterations finished qdiffx linear iterations at : 08:33:57 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.4943554E-04 1.8352509E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 08:33:58 3.446u 0.158s 0:04.32 83.1% 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 08:33:58 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 = 2086 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.103687 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): -19.56200 26.14400 ymin,ymax (A): -12.58200 28.37800 zmin,zma (A): -2.379000 48.38900 x,y,z range (A): 45.70600 40.96000 50.76800 scale (grids/A): 2.103687 object centre (A): 3.290999 7.898000 23.00500 number of atom coordinates read : 2086 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 87.74538 89.48157 90.14726 assigned negative charge : -312.6442 centred at (gu) : 87.43347 89.56452 90.30392 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73112 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17293 grid for indexing accessible points = 1.400000 m= 28770 mr = 51792 m= 5566 mr = 21686 m= 478 mr = 3649 m= 11 mr = 227 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15622 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) : 0.7012291 object centre at (A) : 3.290999 7.898000 23.00500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8096428E-02 6.6683322E-02 midg,1,midg; midg,igrid,midg 2.6857607E-02 6.8324748E-03 1,midg,midg; igrid,midg,midg 8.5306261E-03 2.4962995E-02 gauss-seidel spectral radius is 0.9988111 estimated iterations to convergence 230 setup time was (sec) 0.8600000 now iterating at: 08:33:59 rms-change max change #iterations 4.543293 175.4539 at 10iterations 2.240293 75.30585 at 20iterations 1.101628 33.85834 at 30iterations 0.5472668 16.88229 at 40iterations 0.2697710 8.949419 at 50iterations 0.1332042 4.239792 at 60iterations 6.5681264E-02 2.219683 at 70iterations 3.2420933E-02 1.081116 at 80iterations 1.6042925E-02 0.5250053 at 90iterations 7.9932828E-03 0.2458487 at 100iterations 3.9693755E-03 0.1169710 at 110iterations 1.9974874E-03 7.0240021E-02 at 120iterations finished qdiffx linear iterations at : 08:34:05 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.9974874E-03 7.0240021E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 08:34:06 7.501u 0.178s 0:08.22 93.3% 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 08:34:06 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 = 2086 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.155531 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): -19.56200 26.14400 ymin,ymax (A): -12.58200 28.37800 zmin,zma (A): -2.379000 48.38900 x,y,z range (A): 45.70600 40.96000 50.76800 scale (grids/A): 3.155531 object centre (A): 3.290999 7.898000 23.00500 number of atom coordinates read : 2086 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 86.61811 89.22234 90.22088 assigned negative charge : -312.6442 centred at (gu) : 86.15012 89.34678 90.45588 start vw surface at 0.1500000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 168611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17293 grid for indexing accessible points = 1.400000 m= 90112 mr = 125069 m= 36349 mr = 74517 m= 10502 mr = 29756 m= 1915 mr = 8043 m= 164 mr = 1280 m= 7 mr = 83 m= 0 mr = 1 time to grow re-entrant surface = 0.8799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 68911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 15752 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) : 2.103687 object centre at (A) : 3.290999 7.898000 23.00500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3581390 1.144660 midg,1,midg; midg,igrid,midg 0.2279907 3.6226153E-02 1,midg,midg; igrid,midg,midg 0.1464311 0.1908369 gauss-seidel spectral radius is 0.9992902 estimated iterations to convergence 296 setup time was (sec) 2.140000 now iterating at: 08:34:08 rms-change max change #iterations 10.18465 379.1599 at 10iterations 6.032280 137.0459 at 20iterations 3.558864 66.33614 at 30iterations 2.097567 41.52647 at 40iterations 1.233906 25.93716 at 50iterations 0.7246992 13.21133 at 60iterations 0.4238603 8.992680 at 70iterations 0.2480256 4.801672 at 80iterations 0.1458055 2.510835 at 90iterations 8.5006692E-02 1.995214 at 100iterations 4.9831536E-02 0.9912891 at 110iterations 2.9277997E-02 0.4913673 at 120iterations 1.7291777E-02 0.3289108 at 130iterations 1.0343515E-02 0.1838217 at 140iterations 6.2974123E-03 0.1149826 at 150iterations 3.9637978E-03 7.3268890E-02 at 160iterations 2.6292305E-03 4.7809601E-02 at 170iterations 1.8471060E-03 3.1463623E-02 at 180iterations finished qdiffx linear iterations at : 08:34:19 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 1.8471060E-03 3.1463623E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 08:34:20 12.810u 0.202s 0:13.41 97.0% 0+0k 0+0io 0pf+0w