Mon Oct 10 14:10:34 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 Mon Oct 10 2011 at 14:10:34 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: GLM 11 has a net charge of -0.0940 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: 0.5594581 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): 6.020000 61.81200 ymin,ymax (A): -26.19200 29.29100 zmin,zma (A): -36.17100 27.46200 x,y,z range (A): 55.79200 55.48300 63.63300 scale (grids/A): 0.5594581 object centre (A): 33.91600 1.549500 -4.354501 number of atom coordinates read : 3169 total number of charged atoms : 2986 net assigned charge : 3.406030 assigned positive charge : 476.2447 centred at (gu) : 89.47768 90.17454 90.16257 assigned negative charge : -472.8398 centred at (gu) : 89.44778 90.14854 90.05509 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6579 nv = 96 ne = 84 npr = 61540 no. pairs analyzed = 61540 no. exposed pairs = 4445 no. arc points = 31489 no. surface atoms = 1482 nbur = 1687 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 = 1.540000 m= 299 mr = 3124 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3139 ## 374 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6854696E-10 1.6458888E-09 midg,1,midg; midg,igrid,midg 5.1777367E-11 6.8286987E-10 1,midg,midg; igrid,midg,midg 6.6192989E-12 6.1723832E-10 gauss-seidel spectral radius is 0.9835456 estimated iterations to convergence 64 setup time was (sec) 0.6800000 now iterating at: 14:10:35 rms-change max change #iterations 8.6018614E-02 14.37676 at 10iterations 6.0502733E-03 0.9736719 at 20iterations 4.6340661E-04 7.1996689E-02 at 30iterations 6.0054299E-05 9.1552734E-03 at 40iterations 1.6629128E-05 2.3651123E-03 at 50iterations finished qdiffx linear iterations at : 14:10:39 total time elapsed so far: 4.660000 # loops : 50 mean,max change (kT/e) : 1.6629128E-05 2.3651123E-03 energy calculations done at 4.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.810000 DelPhi exited at 14:10:39 4.819u 0.374s 0:05.66 91.5% 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 Mon Oct 10 2011 at 14:10:39 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: GLM 11 has a net charge of -0.0940 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: 1.678374 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): 6.020000 61.81200 ymin,ymax (A): -26.19200 29.29100 zmin,zma (A): -36.17100 27.46200 x,y,z range (A): 55.79200 55.48300 63.63300 scale (grids/A): 1.678374 object centre (A): 33.91600 1.549500 -4.354501 number of atom coordinates read : 3169 total number of charged atoms : 2986 net assigned charge : 3.406030 assigned positive charge : 476.2447 centred at (gu) : 88.43211 90.52254 90.48662 assigned negative charge : -472.8398 centred at (gu) : 88.34277 90.44496 90.16489 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31489 grid for indexing accessible points = 1.400000 m= 22812 mr = 47166 m= 2712 mr = 15139 m= 96 mr = 1227 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 335 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22976 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) : 0.5594581 object centre at (A) : 33.91600 1.549500 -4.354501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2445370E-03 2.2383677E-02 midg,1,midg; midg,igrid,midg -5.7102754E-03 -9.0963840E-03 1,midg,midg; igrid,midg,midg 1.3194513E-02 3.6498284E-04 gauss-seidel spectral radius is 0.9983271 estimated iterations to convergence 194 setup time was (sec) 0.9200000 now iterating at: 14:10:41 rms-change max change #iterations 3.721386 176.3163 at 10iterations 1.604357 59.01118 at 20iterations 0.6903804 24.89153 at 30iterations 0.2964700 9.993141 at 40iterations 0.1285448 4.460933 at 50iterations 5.5578239E-02 1.991767 at 60iterations 2.3956079E-02 0.8076439 at 70iterations 1.0346913E-02 0.3691607 at 80iterations 4.4662263E-03 0.1511202 at 90iterations 1.9368711E-03 6.3008785E-02 at 100iterations 8.3751552E-04 2.7647018E-02 at 110iterations 3.6418156E-04 1.2578249E-02 at 120iterations finished qdiffx linear iterations at : 14:10:51 total time elapsed so far: 11.43000 # loops : 120 mean,max change (kT/e) : 3.6418156E-04 1.2578249E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 14:10:52 11.592u 0.437s 0:12.65 95.0% 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 Mon Oct 10 2011 at 14:10:52 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 !!! WARNING: GLM 11 has a net charge of -0.0940 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: 2.517561 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): 6.020000 61.81200 ymin,ymax (A): -26.19200 29.29100 zmin,zma (A): -36.17100 27.46200 x,y,z range (A): 55.79200 55.48300 63.63300 scale (grids/A): 2.517561 object centre (A): 33.91600 1.549500 -4.354501 number of atom coordinates read : 3169 total number of charged atoms : 2986 net assigned charge : 3.406030 assigned positive charge : 476.2447 centred at (gu) : 87.64793 90.78345 90.72994 assigned negative charge : -472.8398 centred at (gu) : 87.51412 90.66750 90.24727 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 167826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31489 grid for indexing accessible points = 1.400000 m= 77193 mr = 116042 m= 23389 mr = 59401 m= 4268 mr = 17116 m= 334 mr = 2613 m= 7 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 77740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 23869 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) : 1.678374 object centre at (A) : 33.91600 1.549500 -4.354501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5283743E-02 0.2657419 midg,1,midg; midg,igrid,midg 1.3110576E-02 -0.1813117 1,midg,midg; igrid,midg,midg 0.2754577 2.6557785E-02 gauss-seidel spectral radius is 0.9992044 estimated iterations to convergence 280 setup time was (sec) 1.810000 now iterating at: 14:10:54 rms-change max change #iterations 9.689578 271.1120 at 10iterations 5.678300 150.2184 at 20iterations 3.295801 87.53518 at 30iterations 1.896555 43.60165 at 40iterations 1.090733 28.15439 at 50iterations 0.6218540 16.67127 at 60iterations 0.3553811 9.154912 at 70iterations 0.2020146 4.247206 at 80iterations 0.1145044 2.722750 at 90iterations 6.5001480E-02 1.443647 at 100iterations 3.6810242E-02 0.8007050 at 110iterations 2.0799587E-02 0.4429579 at 120iterations 1.1761036E-02 0.2314258 at 130iterations 6.6470145E-03 0.1355515 at 140iterations 3.7453147E-03 7.3333740E-02 at 150iterations 2.1174082E-03 4.3140411E-02 at 160iterations 1.2007548E-03 2.4250031E-02 at 170iterations 6.7754480E-04 1.3763428E-02 at 180iterations finished qdiffx linear iterations at : 14:11:11 total time elapsed so far: 18.66000 # loops : 180 mean,max change (kT/e) : 6.7754480E-04 1.3763428E-02 energy calculations done at 18.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.81000 DelPhi exited at 14:11:12 18.817u 0.475s 0:19.60 98.3% 0+0k 0+0io 0pf+0w