Sat Oct 8 11:35:16 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 Sat Oct 8 2011 at 11:35:16 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4294 !!! WARNING: HIQ 440 has a net charge of 0.5140 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: 0.5854589 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): -25.59300 35.21400 ymin,ymax (A): 37.82200 97.96200 zmin,zma (A): 31.24200 89.56499 x,y,z range (A): 60.80700 60.14000 58.32300 scale (grids/A): 0.5854589 object centre (A): 4.810498 67.89200 60.40350 number of atom coordinates read : 4294 total number of charged atoms : 4148 net assigned charge : -0.9859650 assigned positive charge : 645.3806 centred at (gu) : 90.60551 87.99542 88.58663 assigned negative charge : -646.3696 centred at (gu) : 90.48808 88.14385 88.71526 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9293 nv = 96 ne = 84 npr = 91472 no. pairs analyzed = 91472 no. exposed pairs = 4679 no. arc points = 31765 no. surface atoms = 1599 nbur = 2695 mkacc time = 0.2400000 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= 402 mr = 5492 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 147 time to turn everything in is 0.4500000 number of dielectric boundary points 4156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3341 ## 360 charges are in solution ## iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 12308 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0832379E-09 -3.9184629E-09 midg,1,midg; midg,igrid,midg 8.1969738E-09 -3.9052348E-09 1,midg,midg; igrid,midg,midg -4.3505235E-09 4.5340380E-09 gauss-seidel spectral radius is 0.9850282 estimated iterations to convergence 67 setup time was (sec) 1.470000 now iterating at: 11:35:18 rms-change max change #iterations 0.1269603 14.73822 at 10iterations 1.0374499E-02 1.387611 at 20iterations 9.9318183E-04 0.1245728 at 30iterations 1.6022794E-04 2.0939827E-02 at 40iterations 4.5660883E-05 6.2103271E-03 at 50iterations finished qdiffx linear iterations at : 11:35:21 total time elapsed so far: 4.750000 # loops : 50 mean,max change (kT/e) : 4.5660883E-05 6.2103271E-03 energy calculations done at 4.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.930000 DelPhi exited at 11:35:22 4.933u 0.428s 0:05.64 94.8% 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 Sat Oct 8 2011 at 11:35:22 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4294 !!! WARNING: HIQ 440 has a net charge of 0.5140 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: 1.756377 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): -25.59300 35.21400 ymin,ymax (A): 37.82200 97.96200 zmin,zma (A): 31.24200 89.56499 x,y,z range (A): 60.80700 60.14000 58.32300 scale (grids/A): 1.756377 object centre (A): 4.810498 67.89200 60.40350 number of atom coordinates read : 4294 total number of charged atoms : 4148 net assigned charge : -0.9859650 assigned positive charge : 645.3806 centred at (gu) : 91.81545 83.98503 85.75875 assigned negative charge : -646.3696 centred at (gu) : 91.46386 84.43112 86.14518 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 103229 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31765 grid for indexing accessible points = 1.400000 m= 35404 mr = 75475 m= 4732 mr = 26521 m= 176 mr = 2953 m= 0 mr = 43 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 5488 time to turn everything in is 0.7800000 number of dielectric boundary points 38549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 301 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 32231 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) : 0.5854589 object centre at (A) : 4.810498 67.89200 60.40350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.0787140E-02 -2.8362390E-02 midg,1,midg; midg,igrid,midg 4.5781150E-02 -7.6851053E-03 1,midg,midg; igrid,midg,midg -1.5373104E-02 3.2528263E-02 gauss-seidel spectral radius is 0.9985384 estimated iterations to convergence 207 setup time was (sec) 1.080000 now iterating at: 11:35:23 rms-change max change #iterations 4.832518 156.3789 at 10iterations 2.204327 63.28400 at 20iterations 1.005839 27.76227 at 30iterations 0.4605793 13.79801 at 40iterations 0.2111029 5.885774 at 50iterations 9.6306086E-02 2.774208 at 60iterations 4.4208527E-02 1.191833 at 70iterations 2.0237898E-02 0.5503511 at 80iterations 9.2903534E-03 0.2402267 at 90iterations 4.2678458E-03 0.1190128 at 100iterations 1.9663081E-03 5.9957504E-02 at 110iterations 9.2114846E-04 2.6320457E-02 at 120iterations finished qdiffx linear iterations at : 11:35:32 total time elapsed so far: 9.630000 # loops : 120 mean,max change (kT/e) : 9.2114846E-04 2.6320457E-02 energy calculations done at 9.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 11:35:32 9.798u 0.478s 0:10.66 96.2% 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 Sat Oct 8 2011 at 11:35:32 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4294 !!! WARNING: HIQ 440 has a net charge of 0.5140 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: 2.634565 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): -25.59300 35.21400 ymin,ymax (A): 37.82200 97.96200 zmin,zma (A): 31.24200 89.56499 x,y,z range (A): 60.80700 60.14000 58.32300 scale (grids/A): 2.634565 object centre (A): 4.810498 67.89200 60.40350 number of atom coordinates read : 4294 total number of charged atoms : 4148 net assigned charge : -0.9859650 assigned positive charge : 645.3806 centred at (gu) : 92.72283 80.97728 83.63769 assigned negative charge : -646.3696 centred at (gu) : 92.19568 81.64663 84.21774 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 240216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31765 grid for indexing accessible points = 1.400000 m= 119394 mr = 183095 m= 38915 mr = 99176 m= 8130 mr = 31551 m= 889 mr = 6204 m= 29 mr = 550 m= 0 mr = 7 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 18438 time to turn everything in is 2.060000 number of dielectric boundary points 86990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 2.200000 number of grid points assigned charge 33178 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) : 1.756377 object centre at (A) : 4.810498 67.89200 60.40350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8347906 -0.3190650 midg,1,midg; midg,igrid,midg 0.5675051 -0.1231375 1,midg,midg; igrid,midg,midg -0.2601863 0.2649060 gauss-seidel spectral radius is 0.9992554 estimated iterations to convergence 289 setup time was (sec) 2.400000 now iterating at: 11:35:35 rms-change max change #iterations 11.69111 414.8732 at 10iterations 6.824109 143.2399 at 20iterations 3.957271 66.36203 at 30iterations 2.295196 45.06300 at 40iterations 1.323382 25.71947 at 50iterations 0.7651244 12.88652 at 60iterations 0.4403656 7.284647 at 70iterations 0.2539136 3.978355 at 80iterations 0.1462259 2.225357 at 90iterations 8.4055863E-02 1.349186 at 100iterations 4.8290670E-02 0.7916384 at 110iterations 2.7774263E-02 0.4405746 at 120iterations 1.6002204E-02 0.2482071 at 130iterations 9.2246057E-03 0.1454544 at 140iterations 5.3258860E-03 8.9588165E-02 at 150iterations 3.0906280E-03 5.2614212E-02 at 160iterations 1.8061360E-03 2.8234959E-02 at 170iterations 1.0712261E-03 1.7571449E-02 at 180iterations finished qdiffx linear iterations at : 11:35:50 total time elapsed so far: 17.24000 # loops : 180 mean,max change (kT/e) : 1.0712261E-03 1.7571449E-02 energy calculations done at 17.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.42000 DelPhi exited at 11:35:51 17.422u 0.482s 0:18.20 98.3% 0+0k 0+0io 0pf+0w