Tue Oct 11 01:09:10 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 01:09:10 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 = 2733 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6193243 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): -6.046000 51.43600 ymin,ymax (A): -15.90700 28.58500 zmin,zma (A): 58.66600 110.9410 x,y,z range (A): 57.48200 44.49200 52.27500 scale (grids/A): 0.6193243 object centre (A): 22.69500 6.339001 84.80350 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.500017 assigned positive charge : 411.6575 centred at (gu) : 89.91187 90.29713 89.46935 assigned negative charge : -407.1582 centred at (gu) : 90.17791 90.20660 89.49039 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6965 nv = 96 ne = 84 npr = 55357 no. pairs analyzed = 55357 no. exposed pairs = 3198 no. arc points = 22814 no. surface atoms = 1084 nbur = 1649 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 343 mr = 3943 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 125 time to turn everything in is 0.3100000 number of dielectric boundary points 3330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2169 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5739742E-09 1.8748612E-09 midg,1,midg; midg,igrid,midg -2.5371620E-09 1.0317493E-08 1,midg,midg; igrid,midg,midg 2.1617984E-08 -1.4920605E-08 gauss-seidel spectral radius is 0.9865085 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 01:09:11 rms-change max change #iterations 0.1328696 18.71150 at 10iterations 1.2875083E-02 2.187330 at 20iterations 1.6719598E-03 0.3263512 at 30iterations 4.0229273E-04 9.1064453E-02 at 40iterations 1.1339460E-04 2.6630402E-02 at 50iterations finished qdiffx linear iterations at : 01:09:13 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.1339460E-04 2.6630402E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 01:09:14 3.367u 0.162s 0:04.07 86.4% 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 Tue Oct 11 2011 at 01:09:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 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: 1.857973 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): -6.046000 51.43600 ymin,ymax (A): -15.90700 28.58500 zmin,zma (A): 58.66600 110.9410 x,y,z range (A): 57.48200 44.49200 52.27500 scale (grids/A): 1.857973 object centre (A): 22.69500 6.339001 84.80350 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.500017 assigned positive charge : 411.6575 centred at (gu) : 89.73471 90.89089 88.40742 assigned negative charge : -407.1582 centred at (gu) : 90.53333 90.61957 88.47076 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22814 grid for indexing accessible points = 1.400000 m= 26651 mr = 53410 m= 3887 mr = 19919 m= 176 mr = 2382 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 3938 time to turn everything in is 0.5900000 number of dielectric boundary points 30897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20285 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) : 0.6193243 object centre at (A) : 22.69500 6.339001 84.80350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1502996E-04 6.0511208E-03 midg,1,midg; midg,igrid,midg 9.4664637E-03 1.7639581E-02 1,midg,midg; igrid,midg,midg 3.8282767E-02 -3.6563270E-02 gauss-seidel spectral radius is 0.9985791 estimated iterations to convergence 210 setup time was (sec) 0.8700000 now iterating at: 01:09:15 rms-change max change #iterations 4.125359 174.0038 at 10iterations 1.891725 73.22789 at 20iterations 0.8724192 32.21785 at 30iterations 0.4020755 14.03356 at 40iterations 0.1856880 6.109838 at 50iterations 8.6078256E-02 2.678467 at 60iterations 3.9755523E-02 1.269760 at 70iterations 1.8512499E-02 0.5835114 at 80iterations 8.7045794E-03 0.2783928 at 90iterations 4.1456842E-03 0.1678162 at 100iterations 2.0618888E-03 8.0015182E-02 at 110iterations 1.0825746E-03 4.1515350E-02 at 120iterations finished qdiffx linear iterations at : 01:09:22 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.0825746E-03 4.1515350E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 01:09:22 7.522u 0.201s 0:08.06 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 Tue Oct 11 2011 at 01:09:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.786959 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): -6.046000 51.43600 ymin,ymax (A): -15.90700 28.58500 zmin,zma (A): 58.66600 110.9410 x,y,z range (A): 57.48200 44.49200 52.27500 scale (grids/A): 2.786959 object centre (A): 22.69500 6.339001 84.80350 number of atom coordinates read : 2733 total number of charged atoms : 2589 net assigned charge : 4.500017 assigned positive charge : 411.6575 centred at (gu) : 89.60191 91.33607 87.61098 assigned negative charge : -407.1582 centred at (gu) : 90.79993 90.92922 87.70617 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 175799 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22814 grid for indexing accessible points = 1.400000 m= 87906 mr = 129438 m= 30267 mr = 72474 m= 6815 mr = 24531 m= 865 mr = 5171 m= 32 mr = 559 m= 0 mr = 7 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 13596 time to turn everything in is 1.420000 number of dielectric boundary points 69504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 20712 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) : 1.857973 object centre at (A) : 22.69500 6.339001 84.80350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6301269E-02 3.0644080E-02 midg,1,midg; midg,igrid,midg 0.1516129 0.2112976 1,midg,midg; igrid,midg,midg 0.4285898 -0.3448895 gauss-seidel spectral radius is 0.9992400 estimated iterations to convergence 286 setup time was (sec) 1.720000 now iterating at: 01:09:24 rms-change max change #iterations 9.799366 349.6895 at 10iterations 5.681894 124.8347 at 20iterations 3.276182 68.00430 at 30iterations 1.877395 36.28336 at 40iterations 1.077621 19.85524 at 50iterations 0.6164749 11.28241 at 60iterations 0.3530493 6.581200 at 70iterations 0.2013946 3.603096 at 80iterations 0.1151904 2.540550 at 90iterations 6.5954745E-02 1.148706 at 100iterations 3.7645526E-02 0.6468124 at 110iterations 2.1570645E-02 0.3721313 at 120iterations 1.2443004E-02 0.2347336 at 130iterations 7.2487765E-03 0.1384735 at 140iterations 4.2836890E-03 8.4091187E-02 at 150iterations 2.6063290E-03 5.9551239E-02 at 160iterations 1.6592999E-03 4.0679932E-02 at 170iterations 1.1186627E-03 2.9411316E-02 at 180iterations finished qdiffx linear iterations at : 01:09:34 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 1.1186627E-03 2.9411316E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 01:09:35 11.967u 0.183s 0:12.84 94.5% 0+0k 0+0io 0pf+0w