Tue Oct 11 06:01:48 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 06:01:48 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7112318 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): 25.86000 72.64100 ymin,ymax (A): -18.63200 31.42200 zmin,zma (A): 4.252000 46.54500 x,y,z range (A): 46.78100 50.05400 42.29300 scale (grids/A): 0.7112318 object centre (A): 49.25050 6.395000 25.39850 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 89.11643 90.17603 90.21582 assigned negative charge : -319.4310 centred at (gu) : 89.25601 90.10523 90.29823 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7245 nv = 96 ne = 84 npr = 42543 no. pairs analyzed = 42543 no. exposed pairs = 2598 no. arc points = 17667 no. surface atoms = 885 nbur = 1433 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 501 mr = 4208 m= 3 mr = 96 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 0.2700000 number of dielectric boundary points 3445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1612 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7984 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5156821E-08 8.6427159E-09 midg,1,midg; midg,igrid,midg 1.4511519E-08 9.6077009E-08 1,midg,midg; igrid,midg,midg 1.5438316E-07 -1.9458664E-08 gauss-seidel spectral radius is 0.9896970 estimated iterations to convergence 80 setup time was (sec) 0.5600000 now iterating at: 06:01:49 rms-change max change #iterations 0.2091347 30.25977 at 10iterations 2.6304450E-02 3.774387 at 20iterations 3.5807597E-03 0.4640903 at 30iterations 6.1676116E-04 8.2280636E-02 at 40iterations 1.6006858E-04 1.8987656E-02 at 50iterations finished qdiffx linear iterations at : 06:01:53 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 1.6006858E-04 1.8987656E-02 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 06:01:53 4.516u 0.378s 0:05.17 94.3% 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 06:01:53 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.133696 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): 25.86000 72.64100 ymin,ymax (A): -18.63200 31.42200 zmin,zma (A): 4.252000 46.54500 x,y,z range (A): 46.78100 50.05400 42.29300 scale (grids/A): 2.133696 object centre (A): 49.25050 6.395000 25.39850 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 87.34929 90.52818 90.64742 assigned negative charge : -319.4310 centred at (gu) : 87.76793 90.31582 90.89458 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17667 grid for indexing accessible points = 1.400000 m= 31573 mr = 54972 m= 6285 mr = 24159 m= 571 mr = 4246 m= 15 mr = 274 m= 0 mr = 3 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 31707 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15783 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) : 0.7112318 object centre at (A) : 49.25050 6.395000 25.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1253686E-02 2.9648768E-02 midg,1,midg; midg,igrid,midg 4.0423080E-02 2.8913233E-02 1,midg,midg; igrid,midg,midg 4.5808151E-02 -5.6155223E-02 gauss-seidel spectral radius is 0.9988453 estimated iterations to convergence 233 setup time was (sec) 0.9500000 now iterating at: 06:01:55 rms-change max change #iterations 4.706318 213.1845 at 10iterations 2.340513 78.21188 at 20iterations 1.165532 38.91309 at 30iterations 0.5811942 16.70511 at 40iterations 0.2909133 8.610188 at 50iterations 0.1444033 4.108421 at 60iterations 7.2070830E-02 2.103733 at 70iterations 3.6149569E-02 1.071993 at 80iterations 1.8101431E-02 0.5597887 at 90iterations 9.1421315E-03 0.2731323 at 100iterations 4.6412218E-03 0.1300659 at 110iterations 2.4151348E-03 7.6245308E-02 at 120iterations finished qdiffx linear iterations at : 06:02:05 total time elapsed so far: 10.96000 # loops : 120 mean,max change (kT/e) : 2.4151348E-03 7.6245308E-02 energy calculations done at 10.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 06:02:06 11.122u 0.443s 0:12.92 89.4% 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 06:02:06 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.200543 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): 25.86000 72.64100 ymin,ymax (A): -18.63200 31.42200 zmin,zma (A): 4.252000 46.54500 x,y,z range (A): 46.78100 50.05400 42.29300 scale (grids/A): 3.200543 object centre (A): 49.25050 6.395000 25.39850 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3760 centred at (gu) : 86.02393 90.79230 90.97115 assigned negative charge : -319.4310 centred at (gu) : 86.65182 90.47364 91.34183 start vw surface at 0.1200000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 177060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17667 grid for indexing accessible points = 1.400000 m= 97741 mr = 131983 m= 40717 mr = 81797 m= 11882 mr = 33581 m= 2430 mr = 9306 m= 320 mr = 1760 m= 20 mr = 224 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 71512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15904 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) : 2.133696 object centre at (A) : 49.25050 6.395000 25.39850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1104342 0.2237282 midg,1,midg; midg,igrid,midg 0.3322055 0.1452257 1,midg,midg; igrid,midg,midg 0.4629867 -0.6830810 gauss-seidel spectral radius is 0.9992993 estimated iterations to convergence 298 setup time was (sec) 2.360000 now iterating at: 06:02:09 rms-change max change #iterations 10.45421 346.1988 at 10iterations 6.194451 136.8758 at 20iterations 3.668360 87.29553 at 30iterations 2.166975 42.44976 at 40iterations 1.277078 23.38770 at 50iterations 0.7513549 13.09321 at 60iterations 0.4421102 8.185632 at 70iterations 0.2595243 4.631713 at 80iterations 0.1528177 2.548871 at 90iterations 8.9719661E-02 1.477521 at 100iterations 5.2721739E-02 0.9318180 at 110iterations 3.1133726E-02 0.5377264 at 120iterations 1.8536491E-02 0.3228302 at 130iterations 1.1221016E-02 0.2053833 at 140iterations 6.9630896E-03 0.1341095 at 150iterations 4.4780504E-03 8.6494446E-02 at 160iterations 3.0385815E-03 6.6673279E-02 at 170iterations 2.1821875E-03 4.5600891E-02 at 180iterations finished qdiffx linear iterations at : 06:02:26 total time elapsed so far: 19.30000 # loops : 180 mean,max change (kT/e) : 2.1821875E-03 4.5600891E-02 energy calculations done at 19.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.45000 DelPhi exited at 06:02:27 19.459u 0.480s 0:20.66 96.4% 0+0k 0+0io 0pf+0w