Tue Oct 11 06:09:51 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 Tue Oct 11 2011 at 06:09:51 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7128268 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): -18.54300 26.10800 ymin,ymax (A): -12.25400 28.33800 zmin,zma (A): -3.122000 46.82000 x,y,z range (A): 44.65100 40.59200 49.94200 scale (grids/A): 0.7128268 object centre (A): 3.782499 8.042001 21.84900 number of atom coordinates read : 2124 total number of charged atoms : 1994 net assigned charge : 6.039011 assigned positive charge : 328.6860 centred at (gu) : 88.97680 89.69831 90.94758 assigned negative charge : -322.6470 centred at (gu) : 88.85225 89.72869 91.03118 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7205 nv = 96 ne = 84 npr = 43030 no. pairs analyzed = 43030 no. exposed pairs = 2536 no. arc points = 17060 no. surface atoms = 869 nbur = 1255 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4202 m= 2 mr = 85 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 0.2800000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1602 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7990 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9076458E-08 1.2012902E-08 midg,1,midg; midg,igrid,midg 8.0986460E-08 3.9333504E-08 1,midg,midg; igrid,midg,midg -1.7356838E-08 1.0665919E-07 gauss-seidel spectral radius is 0.9897400 estimated iterations to convergence 80 setup time was (sec) 0.6000000 now iterating at: 06:09:52 rms-change max change #iterations 0.2071405 26.06165 at 10iterations 2.7014736E-02 3.803373 at 20iterations 3.6288770E-03 0.4637852 at 30iterations 5.7752011E-04 8.3953857E-02 at 40iterations 1.3419976E-04 1.9655228E-02 at 50iterations finished qdiffx linear iterations at : 06:09:56 total time elapsed so far: 4.840000 # loops : 50 mean,max change (kT/e) : 1.3419976E-04 1.9655228E-02 energy calculations done at 4.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.000000 DelPhi exited at 06:09:57 5.007u 0.429s 0:05.76 94.0% 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 06:09:57 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.138481 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): -18.54300 26.10800 ymin,ymax (A): -12.25400 28.33800 zmin,zma (A): -3.122000 46.82000 x,y,z range (A): 44.65100 40.59200 49.94200 scale (grids/A): 2.138481 object centre (A): 3.782499 8.042001 21.84900 number of atom coordinates read : 2124 total number of charged atoms : 1994 net assigned charge : 6.039011 assigned positive charge : 328.6860 centred at (gu) : 86.93031 89.09485 92.84272 assigned negative charge : -322.6470 centred at (gu) : 86.55692 89.18587 93.09374 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17060 grid for indexing accessible points = 1.400000 m= 30643 mr = 55242 m= 5987 mr = 23389 m= 532 mr = 3964 m= 22 mr = 264 m= 0 mr = 4 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 31212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15844 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) : 0.7128268 object centre at (A) : 3.782499 8.042001 21.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0300258E-02 5.5291668E-02 midg,1,midg; midg,igrid,midg 3.1364713E-02 2.9523340E-03 1,midg,midg; igrid,midg,midg 1.7449526E-02 3.1479068E-02 gauss-seidel spectral radius is 0.9988467 estimated iterations to convergence 233 setup time was (sec) 1.000000 now iterating at: 06:09:59 rms-change max change #iterations 4.798755 165.0497 at 10iterations 2.393626 70.15862 at 20iterations 1.195153 40.70084 at 30iterations 0.5956816 17.48271 at 40iterations 0.2980962 9.522047 at 50iterations 0.1485716 4.399609 at 60iterations 7.4398644E-02 2.282410 at 70iterations 3.7187353E-02 1.110352 at 80iterations 1.8560091E-02 0.5507264 at 90iterations 9.3659842E-03 0.2719345 at 100iterations 4.7108103E-03 0.1433942 at 110iterations 2.4086258E-03 7.8702927E-02 at 120iterations finished qdiffx linear iterations at : 06:10:10 total time elapsed so far: 12.30000 # loops : 120 mean,max change (kT/e) : 2.4086258E-03 7.8702927E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 06:10:10 12.467u 0.510s 0:13.30 97.5% 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 Tue Oct 11 2011 at 06:10:10 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.207721 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): -18.54300 26.10800 ymin,ymax (A): -12.25400 28.33800 zmin,zma (A): -3.122000 46.82000 x,y,z range (A): 44.65100 40.59200 49.94200 scale (grids/A): 3.207721 object centre (A): 3.782499 8.042001 21.84900 number of atom coordinates read : 2124 total number of charged atoms : 1994 net assigned charge : 6.039011 assigned positive charge : 328.6860 centred at (gu) : 85.39556 88.64229 94.26407 assigned negative charge : -322.6470 centred at (gu) : 84.83539 88.77872 94.64064 start vw surface at 0.1100000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 177041 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17060 grid for indexing accessible points = 1.400000 m= 95861 mr = 132429 m= 39064 mr = 80179 m= 11487 mr = 32344 m= 2212 mr = 8844 m= 268 mr = 1593 m= 12 mr = 157 m= 0 mr = 5 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.020000 number of dielectric boundary points 70394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 15952 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) : 2.138481 object centre at (A) : 3.782499 8.042001 21.84900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2962704 0.6099239 midg,1,midg; midg,igrid,midg 0.2468647 1.7921668E-03 1,midg,midg; igrid,midg,midg 0.4202794 0.2942358 gauss-seidel spectral radius is 0.9992986 estimated iterations to convergence 298 setup time was (sec) 2.400000 now iterating at: 06:10:13 rms-change max change #iterations 10.62636 306.4896 at 10iterations 6.295682 150.2508 at 20iterations 3.707331 85.49876 at 30iterations 2.190028 48.15728 at 40iterations 1.285453 26.62895 at 50iterations 0.7560711 13.58620 at 60iterations 0.4427367 8.033689 at 70iterations 0.2599166 5.191162 at 80iterations 0.1523833 2.601637 at 90iterations 8.9325428E-02 1.755882 at 100iterations 5.2643988E-02 1.013785 at 110iterations 3.1011533E-02 0.5317307 at 120iterations 1.8416727E-02 0.3344307 at 130iterations 1.1107739E-02 0.1861362 at 140iterations 6.8405154E-03 0.1271830 at 150iterations 4.3661105E-03 7.9037666E-02 at 160iterations 2.9340188E-03 5.1890373E-02 at 170iterations 2.0880052E-03 3.6105990E-02 at 180iterations finished qdiffx linear iterations at : 06:10:31 total time elapsed so far: 20.52000 # loops : 180 mean,max change (kT/e) : 2.0880052E-03 3.6105990E-02 energy calculations done at 20.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.68000 DelPhi exited at 06:10:32 20.689u 0.530s 0:21.51 98.6% 0+0k 0+0io 0pf+0w