Mon Oct 10 14:09:32 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 14:09:32 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2614 !!! WARNING: MG3 365 has a net charge of 1.4000 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: 0.5774814 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): 23.21000 79.97200 ymin,ymax (A): -10.56500 51.08200 zmin,zma (A): 2.807000 54.69000 x,y,z range (A): 56.76200 61.64700 51.88300 scale (grids/A): 0.5774814 object centre (A): 51.59100 20.25850 28.74850 number of atom coordinates read : 2614 total number of charged atoms : 2479 net assigned charge : -1.599989 assigned positive charge : 380.3669 centred at (gu) : 89.10331 88.43391 89.90625 assigned negative charge : -381.9673 centred at (gu) : 89.02095 88.47482 89.84151 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5801 nv = 96 ne = 84 npr = 53482 no. pairs analyzed = 53482 no. exposed pairs = 3302 no. arc points = 23969 no. surface atoms = 1116 nbur = 1498 mkacc time = 0.1300000 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 = 1.484000 m= 278 mr = 2983 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3100000 number of dielectric boundary points 3088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2386 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4782707E-09 7.8067303E-10 midg,1,midg; midg,igrid,midg 5.7954735E-10 -7.1283152E-10 1,midg,midg; igrid,midg,midg -2.1760329E-09 8.8509761E-10 gauss-seidel spectral radius is 0.9844981 estimated iterations to convergence 66 setup time was (sec) 0.5600000 now iterating at: 14:09:33 rms-change max change #iterations 8.8890299E-02 14.99066 at 10iterations 6.8417345E-03 1.019425 at 20iterations 5.2325375E-04 8.4465027E-02 at 30iterations 4.1591531E-05 6.9961548E-03 at 40iterations 3.1348604E-06 5.4645538E-04 at 50iterations finished qdiffx linear iterations at : 14:09:36 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 3.1348604E-06 5.4645538E-04 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 14:09:36 3.631u 0.210s 0:04.20 91.4% 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 Mon Oct 10 2011 at 14:09:36 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2614 !!! WARNING: MG3 365 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.732444 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): 23.21000 79.97200 ymin,ymax (A): -10.56500 51.08200 zmin,zma (A): 2.807000 54.69000 x,y,z range (A): 56.76200 61.64700 51.88300 scale (grids/A): 1.732444 object centre (A): 51.59100 20.25850 28.74850 number of atom coordinates read : 2614 total number of charged atoms : 2479 net assigned charge : -1.599989 assigned positive charge : 380.3669 centred at (gu) : 87.30935 85.30121 89.71828 assigned negative charge : -381.9673 centred at (gu) : 87.06258 85.42425 89.52428 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23969 grid for indexing accessible points = 1.400000 m= 20100 mr = 42264 m= 2324 mr = 13841 m= 91 mr = 1270 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1951 time to turn everything in is 0.5100000 number of dielectric boundary points 28518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19226 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) : 0.5774814 object centre at (A) : 51.59100 20.25850 28.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1524905E-02 1.4838816E-03 midg,1,midg; midg,igrid,midg 8.2527902E-03 -7.2878081E-04 1,midg,midg; igrid,midg,midg -3.0797545E-02 6.9487449E-03 gauss-seidel spectral radius is 0.9983495 estimated iterations to convergence 195 setup time was (sec) 0.8300000 now iterating at: 14:09:37 rms-change max change #iterations 3.460649 178.7628 at 10iterations 1.499432 53.91906 at 20iterations 0.6503794 23.92805 at 30iterations 0.2814690 11.16860 at 40iterations 0.1219668 4.356409 at 50iterations 5.2824628E-02 1.936536 at 60iterations 2.2903247E-02 0.8341389 at 70iterations 9.9398773E-03 0.3871574 at 80iterations 4.3039308E-03 0.1513090 at 90iterations 1.8689823E-03 6.7210197E-02 at 100iterations 8.1148453E-04 3.0227661E-02 at 110iterations 3.5161091E-04 1.2601852E-02 at 120iterations finished qdiffx linear iterations at : 14:09:44 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 3.5161091E-04 1.2601852E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 14:09:45 7.921u 0.276s 0:08.55 95.7% 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 Mon Oct 10 2011 at 14:09:45 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2614 !!! WARNING: MG3 365 has a net charge of 1.4000 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: 2.598667 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): 23.21000 79.97200 ymin,ymax (A): -10.56500 51.08200 zmin,zma (A): 2.807000 54.69000 x,y,z range (A): 56.76200 61.64700 51.88300 scale (grids/A): 2.598667 object centre (A): 51.59100 20.25850 28.74850 number of atom coordinates read : 2614 total number of charged atoms : 2479 net assigned charge : -1.599989 assigned positive charge : 380.3669 centred at (gu) : 85.96391 82.95168 89.57733 assigned negative charge : -381.9673 centred at (gu) : 85.59377 83.13624 89.28629 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 146926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23969 grid for indexing accessible points = 1.400000 m= 68049 mr = 103248 m= 20795 mr = 53894 m= 3920 mr = 15781 m= 388 mr = 2739 m= 11 mr = 192 m= 0 mr = 1 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 6536 time to turn everything in is 1.190000 number of dielectric boundary points 64234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 19825 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) : 1.732444 object centre at (A) : 51.59100 20.25850 28.74850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2110833 1.2483722E-02 midg,1,midg; midg,igrid,midg 0.1426741 -0.1365063 1,midg,midg; igrid,midg,midg -0.4870099 8.6408764E-02 gauss-seidel spectral radius is 0.9991772 estimated iterations to convergence 275 setup time was (sec) 1.530000 now iterating at: 14:09:47 rms-change max change #iterations 8.620152 271.3026 at 10iterations 4.869568 124.2829 at 20iterations 2.727129 60.13372 at 30iterations 1.527889 42.08424 at 40iterations 0.8518624 18.74170 at 50iterations 0.4750025 9.197769 at 60iterations 0.2654573 6.557663 at 70iterations 0.1476451 3.177622 at 80iterations 8.2035713E-02 1.798965 at 90iterations 4.5570113E-02 0.9505024 at 100iterations 2.5362952E-02 0.4782401 at 110iterations 1.4088149E-02 0.2980824 at 120iterations 7.8344736E-03 0.1485889 at 130iterations 4.3598423E-03 8.5499644E-02 at 140iterations 2.4207542E-03 4.8800349E-02 at 150iterations 1.3451793E-03 2.7881622E-02 at 160iterations 7.4892270E-04 1.3893127E-02 at 170iterations 4.1667576E-04 9.0408325E-03 at 180iterations finished qdiffx linear iterations at : 14:09:58 total time elapsed so far: 12.58000 # loops : 180 mean,max change (kT/e) : 4.1667576E-04 9.0408325E-03 energy calculations done at 12.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 14:09:58 12.787u 0.215s 0:13.42 96.7% 0+0k 0+0io 0pf+0w