Sun Oct 9 15:31:55 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 Sun Oct 9 2011 at 15:31:55 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 = 5705 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: 0.5084915 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): 154.2930 224.3040 ymin,ymax (A): 91.20400 154.4660 zmin,zma (A): -0.7020000 67.74800 x,y,z range (A): 70.01100 63.26200 68.45000 scale (grids/A): 0.5084915 object centre (A): 189.2985 122.8350 33.52300 number of atom coordinates read : 5705 total number of charged atoms : 5534 net assigned charge : -1.499966 assigned positive charge : 872.2070 centred at (gu) : 89.84900 89.17548 89.75040 assigned negative charge : -873.7148 centred at (gu) : 89.91391 89.22610 89.64656 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 9031 nv = 96 ne = 84 npr = 117958 no. pairs analyzed = 117958 no. exposed pairs = 6586 no. arc points = 45224 no. surface atoms = 2196 nbur = 3509 mkacc time = 0.2000000 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 = 1.680000 m= 272 mr = 4967 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3900000 number of dielectric boundary points 4333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4339 ## 629 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 12264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4785785E-10 2.5889543E-10 midg,1,midg; midg,igrid,midg 1.5731624E-10 -1.3471523E-10 1,midg,midg; igrid,midg,midg 1.7348763E-10 -2.0155459E-10 gauss-seidel spectral radius is 0.9802738 estimated iterations to convergence 59 setup time was (sec) 0.5800000 now iterating at: 15:31:56 rms-change max change #iterations 7.2972387E-02 12.16073 at 10iterations 4.7461824E-03 0.7831345 at 20iterations 6.7892997E-04 0.1042404 at 30iterations 1.7070207E-04 2.4076462E-02 at 40iterations 4.8722450E-05 6.0691833E-03 at 50iterations finished qdiffx linear iterations at : 15:31:59 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 4.8722450E-05 6.0691833E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 15:31:59 3.671u 0.160s 0:04.19 91.4% 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 Sun Oct 9 2011 at 15:31:59 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 = 5705 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: 1.525475 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): 154.2930 224.3040 ymin,ymax (A): 91.20400 154.4660 zmin,zma (A): -0.7020000 67.74800 x,y,z range (A): 70.01100 63.26200 68.45000 scale (grids/A): 1.525475 object centre (A): 189.2985 122.8350 33.52300 number of atom coordinates read : 5705 total number of charged atoms : 5534 net assigned charge : -1.499966 assigned positive charge : 872.2070 centred at (gu) : 89.54518 87.52470 89.24972 assigned negative charge : -873.7148 centred at (gu) : 89.74149 87.67805 88.93974 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 103303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45224 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 29362 mr = 73455 m= 2530 mr = 20138 m= 47 mr = 1128 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 4770 time to turn everything in is 0.5000000 number of dielectric boundary points 40521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 578 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 41452 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) : 0.5084915 object centre at (A) : 189.2985 122.8350 33.52300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8811118E-04 2.5066189E-03 midg,1,midg; midg,igrid,midg 5.1566078E-03 -3.3072224E-03 1,midg,midg; igrid,midg,midg -1.7550649E-02 -7.8087216E-03 gauss-seidel spectral radius is 0.9981599 estimated iterations to convergence 185 setup time was (sec) 0.7200000 now iterating at: 15:32:00 rms-change max change #iterations 4.202525 155.5614 at 10iterations 1.746680 54.40030 at 20iterations 0.7241187 20.43347 at 30iterations 0.3011638 9.521397 at 40iterations 0.1253186 3.622066 at 50iterations 5.2286677E-02 1.535282 at 60iterations 2.1748560E-02 0.6341820 at 70iterations 9.0658646E-03 0.2933922 at 80iterations 3.7932177E-03 0.1137218 at 90iterations 1.6046065E-03 4.5188904E-02 at 100iterations 6.8670482E-04 2.1276474E-02 at 110iterations 3.0446955E-04 9.1161728E-03 at 120iterations finished qdiffx linear iterations at : 15:32:08 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 3.0446955E-04 9.1161728E-03 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 15:32:08 8.140u 0.220s 0:08.63 96.8% 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 Sun Oct 9 2011 at 15:32:08 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 = 5705 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: 2.288212 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): 154.2930 224.3040 ymin,ymax (A): 91.20400 154.4660 zmin,zma (A): -0.7020000 67.74800 x,y,z range (A): 70.01100 63.26200 68.45000 scale (grids/A): 2.288212 object centre (A): 189.2985 122.8350 33.52300 number of atom coordinates read : 5705 total number of charged atoms : 5534 net assigned charge : -1.499966 assigned positive charge : 872.2070 centred at (gu) : 89.31732 86.28693 88.87404 assigned negative charge : -873.7148 centred at (gu) : 89.61202 86.51705 88.40948 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 241623 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45224 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 107217 mr = 180235 m= 26515 mr = 85338 m= 3518 mr = 19627 m= 169 mr = 2161 m= 2 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 15866 time to turn everything in is 1.190000 number of dielectric boundary points 91615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 44152 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) : 1.525475 object centre at (A) : 189.2985 122.8350 33.52300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1429369 -3.1482283E-02 midg,1,midg; midg,igrid,midg 0.1238397 -7.8630738E-02 1,midg,midg; igrid,midg,midg -0.3945613 -0.1270602 gauss-seidel spectral radius is 0.9991890 estimated iterations to convergence 277 setup time was (sec) 1.450000 now iterating at: 15:32:10 rms-change max change #iterations 11.33122 297.2205 at 10iterations 6.543126 143.8771 at 20iterations 3.738272 105.1506 at 30iterations 2.130513 42.83418 at 40iterations 1.207879 23.20897 at 50iterations 0.6842337 13.33322 at 60iterations 0.3862031 7.315796 at 70iterations 0.2179202 4.721733 at 80iterations 0.1225915 2.413143 at 90iterations 6.9043875E-02 1.157799 at 100iterations 3.8798179E-02 0.6396065 at 110iterations 2.1822874E-02 0.4202824 at 120iterations 1.2238973E-02 0.2271500 at 130iterations 6.8700877E-03 0.1335411 at 140iterations 3.8563784E-03 6.1290741E-02 at 150iterations 2.1673876E-03 3.7697554E-02 at 160iterations 1.2171807E-03 2.1753311E-02 at 170iterations 6.8341766E-04 1.1491776E-02 at 180iterations finished qdiffx linear iterations at : 15:32:22 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 6.8341766E-04 1.1491776E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.45000 DelPhi exited at 15:32:22 13.456u 0.206s 0:14.01 97.4% 0+0k 0+0io 0pf+0w