Sat Oct 15 12:59:45 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 Sat Oct 15 2011 at 12:59:45 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6449626 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): -4.375000 46.35500 ymin,ymax (A): 10.22200 56.37500 zmin,zma (A): 10.16400 65.36100 x,y,z range (A): 50.73000 46.15300 55.19700 scale (grids/A): 0.6449626 object centre (A): 20.99000 33.29850 37.76250 number of atom coordinates read : 2752 total number of charged atoms : 2388 net assigned charge : 8.500018 assigned positive charge : 380.3300 centred at (gu) : 89.27438 91.33984 89.95651 assigned negative charge : -371.8307 centred at (gu) : 89.18869 91.26469 89.83352 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7131 nv = 96 ne = 84 npr = 50572 no. pairs analyzed = 50572 no. exposed pairs = 3187 no. arc points = 22492 no. surface atoms = 1062 nbur = 1690 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3881 m= 4 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2239 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8434 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7265920E-09 2.9403884E-08 midg,1,midg; midg,igrid,midg 3.5670549E-09 3.1462868E-08 1,midg,midg; igrid,midg,midg 3.5616270E-09 2.1500274E-08 gauss-seidel spectral radius is 0.9875396 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 12:59:45 rms-change max change #iterations 0.1457298 23.91677 at 10iterations 1.4740961E-02 2.056519 at 20iterations 1.4755009E-03 0.2179203 at 30iterations 1.5381709E-04 2.3899078E-02 at 40iterations 1.7810034E-05 2.8591156E-03 at 50iterations finished qdiffx linear iterations at : 12:59:48 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 1.7810034E-05 2.8591156E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 12:59:49 3.510u 0.181s 0:04.04 91.3% 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 15 2011 at 12:59:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.934888 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): -4.375000 46.35500 ymin,ymax (A): 10.22200 56.37500 zmin,zma (A): 10.16400 65.36100 x,y,z range (A): 50.73000 46.15300 55.19700 scale (grids/A): 1.934888 object centre (A): 20.99000 33.29850 37.76250 number of atom coordinates read : 2752 total number of charged atoms : 2388 net assigned charge : 8.500018 assigned positive charge : 380.3300 centred at (gu) : 87.82244 94.01902 89.86901 assigned negative charge : -371.8307 centred at (gu) : 87.56602 93.79388 89.50039 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76828 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22492 grid for indexing accessible points = 1.400000 m= 27511 mr = 53190 m= 4211 mr = 19680 m= 241 mr = 2324 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 33528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18661 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) : 0.6449626 object centre at (A) : 20.99000 33.29850 37.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8440584E-02 4.8062917E-02 midg,1,midg; midg,igrid,midg -1.6485108E-02 2.2996147E-03 1,midg,midg; igrid,midg,midg 2.5449438E-02 4.5238331E-02 gauss-seidel spectral radius is 0.9986753 estimated iterations to convergence 218 setup time was (sec) 0.6100000 now iterating at: 12:59:50 rms-change max change #iterations 4.250851 174.2952 at 10iterations 2.005369 73.02054 at 20iterations 0.9480777 31.47735 at 30iterations 0.4499134 13.66014 at 40iterations 0.2133514 6.976736 at 50iterations 0.1005911 3.057361 at 60iterations 4.7823541E-02 1.397856 at 70iterations 2.2663096E-02 0.7842979 at 80iterations 1.0720709E-02 0.3487425 at 90iterations 5.0943200E-03 0.1674194 at 100iterations 2.4155674E-03 7.6798677E-02 at 110iterations 1.1450900E-03 3.7167072E-02 at 120iterations finished qdiffx linear iterations at : 12:59:57 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 1.1450900E-03 3.7167072E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 12:59:57 8.125u 0.233s 0:08.70 95.9% 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 15 2011 at 12:59:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2752 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.902332 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): -4.375000 46.35500 ymin,ymax (A): 10.22200 56.37500 zmin,zma (A): 10.16400 65.36100 x,y,z range (A): 50.73000 46.15300 55.19700 scale (grids/A): 2.902332 object centre (A): 20.99000 33.29850 37.76250 number of atom coordinates read : 2752 total number of charged atoms : 2388 net assigned charge : 8.500018 assigned positive charge : 380.3300 centred at (gu) : 86.73354 96.02835 89.80342 assigned negative charge : -371.8307 centred at (gu) : 86.34895 95.69090 89.25038 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 177679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22492 grid for indexing accessible points = 1.400000 m= 89326 mr = 129199 m= 31691 mr = 71970 m= 7202 mr = 24518 m= 1016 mr = 5027 m= 67 mr = 564 m= 1 mr = 27 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 75678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 19089 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) : 1.934888 object centre at (A) : 20.99000 33.29850 37.76250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2668175E-02 0.3274966 midg,1,midg; midg,igrid,midg -0.1521524 8.0470145E-03 1,midg,midg; igrid,midg,midg 0.1999345 0.4796078 gauss-seidel spectral radius is 0.9992676 estimated iterations to convergence 292 setup time was (sec) 1.240000 now iterating at: 12:59:59 rms-change max change #iterations 9.958638 445.4635 at 10iterations 5.856940 183.7923 at 20iterations 3.425586 92.98384 at 30iterations 2.000492 57.75466 at 40iterations 1.165442 21.86813 at 50iterations 0.6786965 12.91752 at 60iterations 0.3931323 7.125195 at 70iterations 0.2281189 4.043205 at 80iterations 0.1319622 2.440699 at 90iterations 7.6432608E-02 1.412418 at 100iterations 4.4149000E-02 0.8615780 at 110iterations 2.5512062E-02 0.5223393 at 120iterations 1.4715923E-02 0.2662112 at 130iterations 8.5128676E-03 0.1679134 at 140iterations 4.8987009E-03 0.1010084 at 150iterations 2.8310348E-03 5.1156998E-02 at 160iterations 1.6349270E-03 2.9735565E-02 at 170iterations 9.4278454E-04 1.6597748E-02 at 180iterations finished qdiffx linear iterations at : 13:00:11 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 9.4278454E-04 1.6597748E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 13:00:11 13.287u 0.237s 0:13.85 97.5% 0+0k 0+0io 0pf+0w