Sat Oct 15 12:59:59 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 15 2011 at 12:59:59 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 !!! WARNING: HIR 135 has a net charge of 0.5140 !!! WARNING: SEP 281 has a net charge of -0.4750 !!! WARNING: SEP 286 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: 0.6177017 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): 21.65400 69.89300 ymin,ymax (A): -26.31900 27.68100 zmin,zma (A): -13.29500 44.33800 x,y,z range (A): 48.23900 54.00000 57.63300 scale (grids/A): 0.6177017 object centre (A): 45.77350 0.6809998 15.52150 number of atom coordinates read : 2711 total number of charged atoms : 2568 net assigned charge : 2.564006 assigned positive charge : 411.6325 centred at (gu) : 89.57587 90.10597 89.05180 assigned negative charge : -409.0694 centred at (gu) : 89.45023 90.08407 88.94079 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6793 nv = 96 ne = 84 npr = 54852 no. pairs analyzed = 54852 no. exposed pairs = 3509 no. arc points = 24189 no. surface atoms = 1175 nbur = 1536 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3561 m= 3 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2200000 number of dielectric boundary points 3582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2413 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8422 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.6140631E-09 7.4769986E-09 midg,1,midg; midg,igrid,midg 5.9758498E-10 3.5592247E-09 1,midg,midg; igrid,midg,midg -6.9397044E-09 9.2423589E-09 gauss-seidel spectral radius is 0.9864388 estimated iterations to convergence 70 setup time was (sec) 0.4500000 now iterating at: 12:59:59 rms-change max change #iterations 0.1261432 19.22545 at 10iterations 1.1719396E-02 1.830940 at 20iterations 1.1323759E-03 0.1772919 at 30iterations 1.3120650E-04 2.2491455E-02 at 40iterations 2.8991597E-05 4.7545433E-03 at 50iterations finished qdiffx linear iterations at : 13:00:03 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 2.8991597E-05 4.7545433E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 13:00:03 4.013u 0.243s 0:04.53 93.8% 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 13:00:03 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 !!! WARNING: HIR 135 has a net charge of 0.5140 !!! WARNING: SEP 281 has a net charge of -0.4750 !!! WARNING: SEP 286 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.853105 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): 21.65400 69.89300 ymin,ymax (A): -26.31900 27.68100 zmin,zma (A): -13.29500 44.33800 x,y,z range (A): 48.23900 54.00000 57.63300 scale (grids/A): 1.853105 object centre (A): 45.77350 0.6809998 15.52150 number of atom coordinates read : 2711 total number of charged atoms : 2568 net assigned charge : 2.564006 assigned positive charge : 411.6325 centred at (gu) : 88.72674 90.31706 87.15498 assigned negative charge : -409.0694 centred at (gu) : 88.35051 90.25212 86.82204 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 73172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24189 grid for indexing accessible points = 1.400000 m= 25611 mr = 49520 m= 3882 mr = 18064 m= 229 mr = 2168 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 33080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20137 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) : 0.6177017 object centre at (A) : 45.77350 0.6809998 15.52150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1682081E-02 8.1488732E-03 midg,1,midg; midg,igrid,midg 1.4231695E-02 4.8757209E-03 1,midg,midg; igrid,midg,midg 2.2313676E-03 1.5975174E-02 gauss-seidel spectral radius is 0.9985780 estimated iterations to convergence 210 setup time was (sec) 0.6800000 now iterating at: 13:00:04 rms-change max change #iterations 4.146839 193.9037 at 10iterations 1.902007 70.95285 at 20iterations 0.8734002 28.44099 at 30iterations 0.4038542 12.37091 at 40iterations 0.1853095 6.560678 at 50iterations 8.5130461E-02 2.889153 at 60iterations 3.9268494E-02 1.254730 at 70iterations 1.8171985E-02 0.5980263 at 80iterations 8.3850296E-03 0.2875433 at 90iterations 3.8824556E-03 0.1202507 at 100iterations 1.7902437E-03 5.3302765E-02 at 110iterations 8.2813419E-04 2.9314518E-02 at 120iterations finished qdiffx linear iterations at : 13:00:13 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 8.2813419E-04 2.9314518E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.290000 DelPhi exited at 13:00:13 9.295u 0.345s 0:09.95 96.7% 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 13:00:13 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2711 !!! WARNING: HIR 135 has a net charge of 0.5140 !!! WARNING: SEP 281 has a net charge of -0.4750 !!! WARNING: SEP 286 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.779658 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): 21.65400 69.89300 ymin,ymax (A): -26.31900 27.68100 zmin,zma (A): -13.29500 44.33800 x,y,z range (A): 48.23900 54.00000 57.63300 scale (grids/A): 2.779658 object centre (A): 45.77350 0.6809998 15.52150 number of atom coordinates read : 2711 total number of charged atoms : 2568 net assigned charge : 2.564006 assigned positive charge : 411.6325 centred at (gu) : 88.09003 90.47545 85.73219 assigned negative charge : -409.0694 centred at (gu) : 87.52566 90.37814 85.23299 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 168934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24189 grid for indexing accessible points = 1.400000 m= 83462 mr = 120319 m= 28910 mr = 66483 m= 6735 mr = 22318 m= 899 mr = 4653 m= 52 mr = 558 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.010000 number of dielectric boundary points 74650 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 20537 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) : 1.853105 object centre at (A) : 45.77350 0.6809998 15.52150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7778149 0.1073263 midg,1,midg; midg,igrid,midg 0.1396536 4.1287411E-02 1,midg,midg; igrid,midg,midg 2.6296882E-02 0.1200414 gauss-seidel spectral radius is 0.9992470 estimated iterations to convergence 288 setup time was (sec) 1.310000 now iterating at: 13:00:15 rms-change max change #iterations 10.09777 315.2904 at 10iterations 5.978961 148.2858 at 20iterations 3.498171 79.79489 at 30iterations 2.043174 49.32957 at 40iterations 1.187180 24.21315 at 50iterations 0.6872928 13.79529 at 60iterations 0.3969182 8.253760 at 70iterations 0.2289392 4.490364 at 80iterations 0.1318976 2.543613 at 90iterations 7.5629041E-02 1.420298 at 100iterations 4.3354165E-02 0.8146839 at 110iterations 2.5015129E-02 0.4581022 at 120iterations 1.4348807E-02 0.2831593 at 130iterations 8.2223248E-03 0.1515107 at 140iterations 4.7149058E-03 9.5836639E-02 at 150iterations 2.7122966E-03 4.8279762E-02 at 160iterations 1.5561888E-03 2.8593302E-02 at 170iterations 8.9476362E-04 1.8001556E-02 at 180iterations finished qdiffx linear iterations at : 13:00:30 total time elapsed so far: 16.31000 # loops : 180 mean,max change (kT/e) : 8.9476362E-04 1.8001556E-02 energy calculations done at 16.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.44000 DelPhi exited at 13:00:30 16.444u 0.348s 0:17.09 98.1% 0+0k 0+0io 0pf+0w