Tue Oct 11 07:31:14 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 Tue Oct 11 2011 at 07:31:14 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: UMP 565 has a net charge of -0.1000 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: 0.6591494 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): 1.163000 53.31900 ymin,ymax (A): -35.58300 16.11200 zmin,zma (A): 16.55000 70.55900 x,y,z range (A): 52.15600 51.69500 54.00900 scale (grids/A): 0.6591494 object centre (A): 27.24100 -9.735500 43.55450 number of atom coordinates read : 2567 total number of charged atoms : 2425 net assigned charge : -2.599994 assigned positive charge : 378.0722 centred at (gu) : 90.00669 87.58619 90.87149 assigned negative charge : -380.6726 centred at (gu) : 90.11721 87.51240 90.83535 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7591 nv = 96 ne = 84 npr = 53660 no. pairs analyzed = 53660 no. exposed pairs = 3064 no. arc points = 20646 no. surface atoms = 1057 nbur = 1510 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 4468 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 0.3500000 number of dielectric boundary points 3465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1922 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0800541E-08 9.2478203E-10 midg,1,midg; midg,igrid,midg -3.3537770E-08 4.5458459E-09 1,midg,midg; igrid,midg,midg 1.4480952E-08 -2.7196277E-08 gauss-seidel spectral radius is 0.9880648 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 07:31:15 rms-change max change #iterations 0.1621981 29.05630 at 10iterations 1.7178996E-02 2.251873 at 20iterations 1.8918151E-03 0.2574501 at 30iterations 2.2524595E-04 2.9067993E-02 at 40iterations 3.5912071E-05 6.1244965E-03 at 50iterations finished qdiffx linear iterations at : 07:31:18 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.5912071E-05 6.1244965E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 07:31:19 4.141u 0.296s 0:04.76 93.0% 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 Tue Oct 11 2011 at 07:31:19 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: UMP 565 has a net charge of -0.1000 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: 1.977448 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): 1.163000 53.31900 ymin,ymax (A): -35.58300 16.11200 zmin,zma (A): 16.55000 70.55900 x,y,z range (A): 52.15600 51.69500 54.00900 scale (grids/A): 1.977448 object centre (A): 27.24100 -9.735500 43.55450 number of atom coordinates read : 2567 total number of charged atoms : 2425 net assigned charge : -2.599994 assigned positive charge : 378.0722 centred at (gu) : 90.01951 82.75822 92.61424 assigned negative charge : -380.6726 centred at (gu) : 90.35133 82.53711 92.50603 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 81094 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20646 grid for indexing accessible points = 1.400000 m= 31713 mr = 58253 m= 5559 mr = 24652 m= 358 mr = 3751 m= 5 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 2737 time to turn everything in is 0.7300000 number of dielectric boundary points 31911 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 19169 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) : 0.6591494 object centre at (A) : 27.24100 -9.735500 43.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8211169E-04 -1.4285355E-02 midg,1,midg; midg,igrid,midg 4.0182598E-02 2.5163282E-02 1,midg,midg; igrid,midg,midg -2.9140882E-02 -3.4341488E-02 gauss-seidel spectral radius is 0.9987180 estimated iterations to convergence 221 setup time was (sec) 1.030000 now iterating at: 07:31:20 rms-change max change #iterations 4.489605 184.9833 at 10iterations 2.156930 68.99229 at 20iterations 1.036098 30.96017 at 30iterations 0.4986357 14.79431 at 40iterations 0.2402222 8.610394 at 50iterations 0.1154453 3.468525 at 60iterations 5.5445183E-02 1.683125 at 70iterations 2.6615458E-02 0.7358761 at 80iterations 1.2751517E-02 0.3828773 at 90iterations 6.1594946E-03 0.1770399 at 100iterations 2.9551387E-03 8.7591171E-02 at 110iterations 1.4244820E-03 4.3262482E-02 at 120iterations finished qdiffx linear iterations at : 07:31:28 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 1.4244820E-03 4.3262482E-02 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 07:31:29 9.718u 0.301s 0:10.64 94.0% 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 Tue Oct 11 2011 at 07:31:29 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: UMP 565 has a net charge of -0.1000 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: 2.966172 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): 1.163000 53.31900 ymin,ymax (A): -35.58300 16.11200 zmin,zma (A): 16.55000 70.55900 x,y,z range (A): 52.15600 51.69500 54.00900 scale (grids/A): 2.966172 object centre (A): 27.24100 -9.735500 43.55450 number of atom coordinates read : 2567 total number of charged atoms : 2425 net assigned charge : -2.599994 assigned positive charge : 378.0722 centred at (gu) : 90.02911 79.13721 93.92116 assigned negative charge : -380.6726 centred at (gu) : 90.52702 78.80566 93.75890 start vw surface at 0.1700000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 187375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20646 grid for indexing accessible points = 1.400000 m= 100399 mr = 140258 m= 39274 mr = 84667 m= 10114 mr = 32856 m= 1745 mr = 7995 m= 135 mr = 1334 m= 0 mr = 69 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 9092 time to turn everything in is 1.910000 number of dielectric boundary points 71863 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 19398 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) : 1.977448 object centre at (A) : 27.24100 -9.735500 43.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1197228 -0.1414982 midg,1,midg; midg,igrid,midg 0.6866405 0.2598745 1,midg,midg; igrid,midg,midg -0.3061254 -9.9803440E-02 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.260000 now iterating at: 07:31:32 rms-change max change #iterations 10.24519 398.2180 at 10iterations 5.985800 118.3428 at 20iterations 3.486792 62.41933 at 30iterations 2.023894 37.82183 at 40iterations 1.174742 24.43097 at 50iterations 0.6833886 11.57861 at 60iterations 0.3949920 7.345074 at 70iterations 0.2288949 4.052311 at 80iterations 0.1324710 2.244415 at 90iterations 7.6731309E-02 1.327774 at 100iterations 4.4314165E-02 0.7437229 at 110iterations 2.5677580E-02 0.4328918 at 120iterations 1.4823761E-02 0.2491722 at 130iterations 8.5725375E-03 0.1368637 at 140iterations 4.9806973E-03 8.3492041E-02 at 150iterations 2.8749844E-03 4.9118996E-02 at 160iterations 1.6723130E-03 3.1173706E-02 at 170iterations 9.7315834E-04 1.5945435E-02 at 180iterations finished qdiffx linear iterations at : 07:31:46 total time elapsed so far: 16.28000 # loops : 180 mean,max change (kT/e) : 9.7315834E-04 1.5945435E-02 energy calculations done at 16.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.46000 DelPhi exited at 07:31:47 16.462u 0.302s 0:17.29 96.9% 0+0k 0+0io 0pf+0w