Mon Oct 10 09:47:34 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 09:47:34 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3030 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5444008 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): 109.8310 175.2240 ymin,ymax (A): -41.99500 10.83400 zmin,zma (A): 46.26700 104.2750 x,y,z range (A): 65.39300 52.82900 58.00800 scale (grids/A): 0.5444008 object centre (A): 142.5275 -15.58050 75.27100 number of atom coordinates read : 3030 total number of charged atoms : 2875 net assigned charge : 6.014017 assigned positive charge : 446.5486 centred at (gu) : 89.96245 88.74315 89.20185 assigned negative charge : -440.5352 centred at (gu) : 90.00171 88.86071 89.02563 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5981 nv = 96 ne = 84 npr = 58223 no. pairs analyzed = 58223 no. exposed pairs = 4651 no. arc points = 33536 no. surface atoms = 1534 nbur = 1496 mkacc time = 0.1000000 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 = 1.540000 m= 256 mr = 2532 m= 1 mr = 14 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 0.2100000 number of dielectric boundary points 3692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3320 ## 432 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7787 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3977082E-10 1.1645673E-09 midg,1,midg; midg,igrid,midg 1.4653302E-09 -2.7844410E-10 1,midg,midg; igrid,midg,midg 5.9963851E-10 1.0694914E-10 gauss-seidel spectral radius is 0.9826277 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 09:47:34 rms-change max change #iterations 7.0881806E-02 13.67385 at 10iterations 4.5713810E-03 1.049393 at 20iterations 3.0899161E-04 4.8162818E-02 at 30iterations 2.4218054E-05 3.8309097E-03 at 40iterations 3.2078365E-06 3.8909912E-04 at 50iterations finished qdiffx linear iterations at : 09:47:37 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.2078365E-06 3.8909912E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:47:38 3.374u 0.164s 0:03.83 92.1% 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 09:47:38 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3030 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.633202 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): 109.8310 175.2240 ymin,ymax (A): -41.99500 10.83400 zmin,zma (A): 46.26700 104.2750 x,y,z range (A): 65.39300 52.82900 58.00800 scale (grids/A): 1.633202 object centre (A): 142.5275 -15.58050 75.27100 number of atom coordinates read : 3030 total number of charged atoms : 2875 net assigned charge : 6.014017 assigned positive charge : 446.5486 centred at (gu) : 89.88681 86.22906 87.60518 assigned negative charge : -440.5352 centred at (gu) : 90.00491 86.58181 87.07624 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33536 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19455 mr = 38829 m= 2081 mr = 12064 m= 71 mr = 857 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.3200000 number of dielectric boundary points 34223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 347 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 22004 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) : 0.5444008 object centre at (A) : 142.5275 -15.58050 75.27100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1651199E-02 2.0786909E-02 midg,1,midg; midg,igrid,midg 1.7907279E-02 3.5678404E-03 1,midg,midg; igrid,midg,midg 3.5643950E-03 -8.0892304E-03 gauss-seidel spectral radius is 0.9982171 estimated iterations to convergence 188 setup time was (sec) 0.5500000 now iterating at: 09:47:38 rms-change max change #iterations 3.307721 163.1263 at 10iterations 1.384256 53.42863 at 20iterations 0.5797692 22.85238 at 30iterations 0.2428673 9.107040 at 40iterations 0.1020776 3.972464 at 50iterations 4.2832799E-02 1.565572 at 60iterations 1.7954394E-02 0.6878015 at 70iterations 7.4664215E-03 0.2682600 at 80iterations 3.1480542E-03 0.1126480 at 90iterations 1.3212292E-03 5.1795959E-02 at 100iterations 5.5639801E-04 1.9801140E-02 at 110iterations 2.3333381E-04 9.5686913E-03 at 120iterations finished qdiffx linear iterations at : 09:47:45 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.3333381E-04 9.5686913E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 09:47:46 7.632u 0.179s 0:08.07 96.6% 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 Mon Oct 10 2011 at 09:47:46 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3030 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.449804 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): 109.8310 175.2240 ymin,ymax (A): -41.99500 10.83400 zmin,zma (A): 46.26700 104.2750 x,y,z range (A): 65.39300 52.82900 58.00800 scale (grids/A): 2.449804 object centre (A): 142.5275 -15.58050 75.27100 number of atom coordinates read : 3030 total number of charged atoms : 2875 net assigned charge : 6.014017 assigned positive charge : 446.5486 centred at (gu) : 89.83006 84.34350 86.40768 assigned negative charge : -440.5352 centred at (gu) : 90.00742 84.87255 85.61420 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 148876 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33536 grid for indexing accessible points = 1.400000 m= 65178 mr = 96157 m= 19346 mr = 48007 m= 3217 mr = 13516 m= 236 mr = 1766 m= 5 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 200 time to turn everything in is 0.7700000 number of dielectric boundary points 77352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 22971 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) : 1.633202 object centre at (A) : 142.5275 -15.58050 75.27100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1787375 0.2945203 midg,1,midg; midg,igrid,midg 0.2628784 6.7039073E-02 1,midg,midg; igrid,midg,midg 1.8881662E-02 -0.1558438 gauss-seidel spectral radius is 0.9991663 estimated iterations to convergence 274 setup time was (sec) 1.010000 now iterating at: 09:47:47 rms-change max change #iterations 8.844640 293.3764 at 10iterations 5.103781 130.1107 at 20iterations 2.897706 78.29490 at 30iterations 1.645837 46.94889 at 40iterations 0.9219651 21.92650 at 50iterations 0.5179569 12.00700 at 60iterations 0.2901341 7.174210 at 70iterations 0.1623807 3.859848 at 80iterations 9.0394430E-02 2.482995 at 90iterations 5.0383285E-02 1.104488 at 100iterations 2.8004227E-02 0.7203951 at 110iterations 1.5577334E-02 0.3621006 at 120iterations 8.6551318E-03 0.1991711 at 130iterations 4.7985706E-03 0.1017228 at 140iterations 2.6618275E-03 5.7793617E-02 at 150iterations 1.4792344E-03 3.0801773E-02 at 160iterations 8.2197727E-04 1.6441822E-02 at 170iterations 4.5546560E-04 9.0484619E-03 at 180iterations finished qdiffx linear iterations at : 09:47:58 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 4.5546560E-04 9.0484619E-03 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 09:47:59 12.211u 0.202s 0:12.84 96.6% 0+0k 0+0io 0pf+0w