Mon Oct 10 14:04:37 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+sph.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 Mon Oct 10 2011 at 14:04:37 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 = 2277 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: 0.6594058 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): -29.78700 22.24800 ymin,ymax (A): 27.59400 70.15500 zmin,zma (A): 14.12500 68.11300 x,y,z range (A): 52.03500 42.56100 53.98800 scale (grids/A): 0.6594058 object centre (A): -3.769500 48.87450 41.11900 number of atom coordinates read : 2277 total number of charged atoms : 2143 net assigned charge : 11.50002 assigned positive charge : 330.9276 centred at (gu) : 91.68399 91.67014 89.20139 assigned negative charge : -319.4282 centred at (gu) : 91.66969 91.59403 89.17358 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6947 nv = 96 ne = 84 npr = 44882 no. pairs analyzed = 44882 no. exposed pairs = 3103 no. arc points = 22412 no. surface atoms = 1033 nbur = 1244 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 473 mr = 3579 m= 2 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3771 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8033185E-08 2.7906513E-08 midg,1,midg; midg,igrid,midg 1.1744532E-08 5.6989560E-08 1,midg,midg; igrid,midg,midg 1.8691296E-08 4.3151068E-08 gauss-seidel spectral radius is 0.9880636 estimated iterations to convergence 75 setup time was (sec) 0.4800000 now iterating at: 14:04:38 rms-change max change #iterations 0.1484043 23.62808 at 10iterations 1.6037486E-02 2.469736 at 20iterations 1.7904014E-03 0.2682018 at 30iterations 2.5512179E-04 4.4111252E-02 at 40iterations 5.2339150E-05 1.1119843E-02 at 50iterations finished qdiffx linear iterations at : 14:04:40 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 5.2339150E-05 1.1119843E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:04:41 3.069u 0.143s 0:03.63 88.1% 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 14:04:41 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 = 2277 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: 1.978217 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): -29.78700 22.24800 ymin,ymax (A): 27.59400 70.15500 zmin,zma (A): 14.12500 68.11300 x,y,z range (A): 52.03500 42.56100 53.98800 scale (grids/A): 1.978217 object centre (A): -3.769500 48.87450 41.11900 number of atom coordinates read : 2277 total number of charged atoms : 2143 net assigned charge : 11.50002 assigned positive charge : 330.9276 centred at (gu) : 95.05186 95.01016 87.60407 assigned negative charge : -319.4282 centred at (gu) : 95.00916 94.78223 87.52087 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22412 grid for indexing accessible points = 1.400000 m= 28026 mr = 49022 m= 5206 mr = 20300 m= 425 mr = 3232 m= 6 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 714 time to turn everything in is 0.5200000 number of dielectric boundary points 34562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 16955 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) : 0.6594058 object centre at (A) : -3.769500 48.87450 41.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7091234E-02 5.2143708E-02 midg,1,midg; midg,igrid,midg -1.8134832E-03 3.5704199E-02 1,midg,midg; igrid,midg,midg 4.9160276E-02 3.0096507E-02 gauss-seidel spectral radius is 0.9987127 estimated iterations to convergence 221 setup time was (sec) 0.7700000 now iterating at: 14:04:42 rms-change max change #iterations 4.137425 210.1482 at 10iterations 1.973961 69.16857 at 20iterations 0.9410019 35.55707 at 30iterations 0.4502718 15.99166 at 40iterations 0.2150755 6.261925 at 50iterations 0.1028619 3.339931 at 60iterations 4.8973508E-02 1.613312 at 70iterations 2.3502221E-02 0.7090149 at 80iterations 1.1246867E-02 0.4216595 at 90iterations 5.3988132E-03 0.1815872 at 100iterations 2.5930456E-03 7.7579498E-02 at 110iterations 1.2571423E-03 3.8860321E-02 at 120iterations finished qdiffx linear iterations at : 14:04:48 total time elapsed so far: 7.050000 # loops : 120 mean,max change (kT/e) : 1.2571423E-03 3.8860321E-02 energy calculations done at 7.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.230000 DelPhi exited at 14:04:49 7.234u 0.160s 0:07.95 92.9% 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 14:04:49 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 = 2277 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.967326 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): -29.78700 22.24800 ymin,ymax (A): 27.59400 70.15500 zmin,zma (A): 14.12500 68.11300 x,y,z range (A): 52.03500 42.56100 53.98800 scale (grids/A): 2.967326 object centre (A): -3.769500 48.87450 41.11900 number of atom coordinates read : 2277 total number of charged atoms : 2143 net assigned charge : 11.50002 assigned positive charge : 330.9276 centred at (gu) : 97.57773 97.51519 86.40596 assigned negative charge : -319.4282 centred at (gu) : 97.51380 97.17342 86.28124 start vw surface at 0.2200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 169870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22412 grid for indexing accessible points = 1.400000 m= 87507 mr = 119257 m= 34622 mr = 70392 m= 9655 mr = 27527 m= 1759 mr = 7212 m= 178 mr = 1229 m= 7 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 2493 time to turn everything in is 1.460000 number of dielectric boundary points 77891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 17144 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) : 1.978217 object centre at (A) : -3.769500 48.87450 41.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6751099 0.4319340 midg,1,midg; midg,igrid,midg -1.3467086E-02 0.3126998 1,midg,midg; igrid,midg,midg 0.7016626 0.2627166 gauss-seidel spectral radius is 0.9992907 estimated iterations to convergence 296 setup time was (sec) 1.750000 now iterating at: 14:04:51 rms-change max change #iterations 9.805850 362.8815 at 10iterations 5.829727 163.7565 at 20iterations 3.464601 78.55905 at 30iterations 2.047447 46.09283 at 40iterations 1.202406 25.53154 at 50iterations 0.7069600 14.24066 at 60iterations 0.4144345 9.274776 at 70iterations 0.2420326 4.954302 at 80iterations 0.1413803 2.616893 at 90iterations 8.2289681E-02 1.519611 at 100iterations 4.7915030E-02 0.9720747 at 110iterations 2.7975967E-02 0.5167267 at 120iterations 1.6281934E-02 0.2955132 at 130iterations 9.4958507E-03 0.1877785 at 140iterations 5.5209775E-03 9.8626137E-02 at 150iterations 3.2175251E-03 5.7048559E-02 at 160iterations 1.8704161E-03 3.1257629E-02 at 170iterations 1.0903446E-03 2.0569801E-02 at 180iterations finished qdiffx linear iterations at : 14:05:00 total time elapsed so far: 11.14000 # loops : 180 mean,max change (kT/e) : 1.0903446E-03 2.0569801E-02 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 14:05:01 11.359u 0.169s 0:11.86 97.0% 0+0k 0+0io 0pf+0w