Wed Feb 15 08:54:45 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:45 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 = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6331478 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): -9.044000 36.33600 ymin,ymax (A): -15.39300 40.83400 zmin,zma (A): 5.426000 52.57000 x,y,z range (A): 45.38000 56.22700 47.14400 scale (grids/A): 0.6331478 object centre (A): 13.64600 12.72050 28.99800 number of atom coordinates read : 2364 total number of charged atoms : 2228 net assigned charge : 4.500007 assigned positive charge : 353.9043 centred at (gu) : 90.55725 89.02145 90.55305 assigned negative charge : -349.4048 centred at (gu) : 90.47704 89.02294 90.69711 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6311 nv = 96 ne = 84 npr = 49041 no. pairs analyzed = 49041 no. exposed pairs = 2874 no. arc points = 19910 no. surface atoms = 984 nbur = 1380 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3507 m= 1 mr = 38 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 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2125 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5727595E-08 -8.2955367E-09 midg,1,midg; midg,igrid,midg 6.8026900E-09 4.3095287E-09 1,midg,midg; igrid,midg,midg -1.4021081E-09 1.3888191E-08 gauss-seidel spectral radius is 0.9870543 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 08:54:46 rms-change max change #iterations 0.1328002 21.42490 at 10iterations 1.2845709E-02 1.957092 at 20iterations 1.3201243E-03 0.2007351 at 30iterations 1.5666302E-04 2.5297165E-02 at 40iterations 2.2972492E-05 3.5896301E-03 at 50iterations finished qdiffx linear iterations at : 08:54:48 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 2.2972492E-05 3.5896301E-03 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 08:54:49 3.146u 0.158s 0:04.12 79.8% 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 Wed Feb 15 2012 at 08:54:50 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 = 2364 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: 1.899443 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): -9.044000 36.33600 ymin,ymax (A): -15.39300 40.83400 zmin,zma (A): 5.426000 52.57000 x,y,z range (A): 45.38000 56.22700 47.14400 scale (grids/A): 1.899443 object centre (A): 13.64600 12.72050 28.99800 number of atom coordinates read : 2364 total number of charged atoms : 2228 net assigned charge : 4.500007 assigned positive charge : 353.9043 centred at (gu) : 91.67152 87.06421 91.65869 assigned negative charge : -349.4048 centred at (gu) : 91.43111 87.06878 92.09113 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67938 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19910 grid for indexing accessible points = 1.400000 m= 24625 mr = 47323 m= 3673 mr = 18164 m= 223 mr = 2256 m= 3 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 537 time to turn everything in is 0.4900000 number of dielectric boundary points 28611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 17516 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) : 0.6331478 object centre at (A) : 13.64600 12.72050 28.99800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2744601E-02 -2.0947374E-02 midg,1,midg; midg,igrid,midg 1.6012827E-02 3.2732610E-02 1,midg,midg; igrid,midg,midg -3.5083173E-03 7.9150638E-03 gauss-seidel spectral radius is 0.9986021 estimated iterations to convergence 212 setup time was (sec) 0.7500000 now iterating at: 08:54:51 rms-change max change #iterations 3.959064 179.8252 at 10iterations 1.848621 62.17107 at 20iterations 0.8612724 26.43276 at 30iterations 0.4011486 13.47680 at 40iterations 0.1864951 5.904491 at 50iterations 8.6785950E-02 2.860257 at 60iterations 4.0374395E-02 1.391682 at 70iterations 1.8783037E-02 0.6359494 at 80iterations 8.7128058E-03 0.3043710 at 90iterations 4.0480988E-03 0.1342616 at 100iterations 1.8832522E-03 6.5673828E-02 at 110iterations 8.7712356E-04 3.2699585E-02 at 120iterations finished qdiffx linear iterations at : 08:54:57 total time elapsed so far: 6.810000 # loops : 120 mean,max change (kT/e) : 8.7712356E-04 3.2699585E-02 energy calculations done at 6.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 08:54:57 6.963u 0.247s 0:07.77 92.6% 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 Wed Feb 15 2012 at 08:54:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 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: 2.849165 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): -9.044000 36.33600 ymin,ymax (A): -15.39300 40.83400 zmin,zma (A): 5.426000 52.57000 x,y,z range (A): 45.38000 56.22700 47.14400 scale (grids/A): 2.849165 object centre (A): 13.64600 12.72050 28.99800 number of atom coordinates read : 2364 total number of charged atoms : 2228 net assigned charge : 4.500007 assigned positive charge : 353.9043 centred at (gu) : 92.50709 85.59622 92.48802 assigned negative charge : -349.4048 centred at (gu) : 92.14658 85.60310 93.13671 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 156730 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19910 grid for indexing accessible points = 1.400000 m= 80365 mr = 114240 m= 28321 mr = 65925 m= 6597 mr = 22749 m= 988 mr = 4952 m= 65 mr = 705 m= 0 mr = 32 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 1852 time to turn everything in is 1.280000 number of dielectric boundary points 64463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17821 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) : 1.899443 object centre at (A) : 13.64600 12.72050 28.99800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3746585 -0.2870982 midg,1,midg; midg,igrid,midg 0.1454732 0.3321398 1,midg,midg; igrid,midg,midg -1.9939704E-02 1.9509923E-02 gauss-seidel spectral radius is 0.9992422 estimated iterations to convergence 287 setup time was (sec) 1.580000 now iterating at: 08:55:03 rms-change max change #iterations 9.355299 335.2653 at 10iterations 5.423324 121.6831 at 20iterations 3.123324 80.39606 at 30iterations 1.794430 37.18292 at 40iterations 1.029877 19.95521 at 50iterations 0.5912569 11.27800 at 60iterations 0.3381083 7.312111 at 70iterations 0.1938370 3.607151 at 80iterations 0.1103820 2.157951 at 90iterations 6.3202754E-02 1.191257 at 100iterations 3.6098305E-02 0.7548447 at 110iterations 2.0579917E-02 0.4097404 at 120iterations 1.1751040E-02 0.2350111 at 130iterations 6.7328964E-03 0.1328335 at 140iterations 3.8372253E-03 7.5344563E-02 at 150iterations 2.2038247E-03 4.0186882E-02 at 160iterations 1.2613500E-03 2.3690701E-02 at 170iterations 7.2718726E-04 1.4347076E-02 at 180iterations finished qdiffx linear iterations at : 08:55:14 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 7.2718726E-04 1.4347076E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 08:55:15 12.040u 0.247s 0:17.36 70.7% 0+0k 0+0io 0pf+0w