Sat Oct 8 11:43:49 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 Sat Oct 8 2011 at 11:43:49 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2427 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: 0.5763968 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): -27.23000 22.06600 ymin,ymax (A): -37.63300 24.13000 zmin,zma (A): -49.43400 6.217000 x,y,z range (A): 49.29600 61.76300 55.65100 scale (grids/A): 0.5763968 object centre (A): -2.582000 -6.751501 -21.60850 number of atom coordinates read : 2427 total number of charged atoms : 2279 net assigned charge : -2.499994 assigned positive charge : 353.9960 centred at (gu) : 89.47158 92.15895 92.07902 assigned negative charge : -356.4963 centred at (gu) : 89.49534 92.15426 91.99467 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5377 nv = 96 ne = 84 npr = 48395 no. pairs analyzed = 48395 no. exposed pairs = 3288 no. arc points = 23362 no. surface atoms = 1105 nbur = 1322 mkacc time = 0.1600000 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 = 1.484000 m= 230 mr = 2634 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2953 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 6778 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1252840E-09 1.3160959E-09 midg,1,midg; midg,igrid,midg -3.5687470E-10 -7.1846390E-10 1,midg,midg; igrid,midg,midg -1.5928478E-10 -7.7738221E-10 gauss-seidel spectral radius is 0.9844275 estimated iterations to convergence 66 setup time was (sec) 0.7000000 now iterating at: 11:43:50 rms-change max change #iterations 8.4318288E-02 15.96061 at 10iterations 6.5366975E-03 1.068424 at 20iterations 5.0872291E-04 8.1033707E-02 at 30iterations 4.3089676E-05 8.2435608E-03 at 40iterations 5.0978974E-06 8.2969666E-04 at 50iterations finished qdiffx linear iterations at : 11:43:53 total time elapsed so far: 4.240000 # loops : 50 mean,max change (kT/e) : 5.0978974E-06 8.2969666E-04 energy calculations done at 4.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 11:43:54 4.453u 0.444s 0:05.17 94.5% 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 8 2011 at 11:43:54 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2427 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: 1.729190 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): -27.23000 22.06600 ymin,ymax (A): -37.63300 24.13000 zmin,zma (A): -49.43400 6.217000 x,y,z range (A): 49.29600 61.76300 55.65100 scale (grids/A): 1.729190 object centre (A): -2.582000 -6.751501 -21.60850 number of atom coordinates read : 2427 total number of charged atoms : 2279 net assigned charge : -2.499994 assigned positive charge : 353.9960 centred at (gu) : 88.41418 96.47625 96.23650 assigned negative charge : -356.4963 centred at (gu) : 88.48570 96.46223 95.98365 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 58697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23362 grid for indexing accessible points = 1.400000 m= 18116 mr = 38298 m= 1991 mr = 12257 m= 63 mr = 1002 m= 0 mr = 16 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 0.6100000 number of dielectric boundary points 27294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17722 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) : 0.5763968 object centre at (A) : -2.582000 -6.751501 -21.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4962176E-03 1.0069310E-02 midg,1,midg; midg,igrid,midg 1.5420417E-03 -1.8307013E-03 1,midg,midg; igrid,midg,midg -4.8267627E-03 -4.5928350E-03 gauss-seidel spectral radius is 0.9983301 estimated iterations to convergence 194 setup time was (sec) 0.9300000 now iterating at: 11:43:55 rms-change max change #iterations 3.325568 152.4814 at 10iterations 1.430258 64.73978 at 20iterations 0.6174037 24.01165 at 30iterations 0.2653373 11.04299 at 40iterations 0.1141464 4.049173 at 50iterations 4.9336579E-02 1.969021 at 60iterations 2.1340599E-02 0.7775421 at 70iterations 9.1784243E-03 0.3510776 at 80iterations 3.9685313E-03 0.1421528 at 90iterations 1.7098672E-03 5.8086514E-02 at 100iterations 7.4230117E-04 2.5832653E-02 at 110iterations 3.2014458E-04 1.1703491E-02 at 120iterations finished qdiffx linear iterations at : 11:44:04 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 3.2014458E-04 1.1703491E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.970000 DelPhi exited at 11:44:05 9.975u 0.470s 0:10.72 97.3% 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 8 2011 at 11:44:05 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2427 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: 2.593786 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): -27.23000 22.06600 ymin,ymax (A): -37.63300 24.13000 zmin,zma (A): -49.43400 6.217000 x,y,z range (A): 49.29600 61.76300 55.65100 scale (grids/A): 2.593786 object centre (A): -2.582000 -6.751501 -21.60850 number of atom coordinates read : 2427 total number of charged atoms : 2279 net assigned charge : -2.499994 assigned positive charge : 353.9960 centred at (gu) : 87.62110 99.71421 99.35467 assigned negative charge : -356.4963 centred at (gu) : 87.72845 99.69329 98.97538 start vw surface at 0.1600000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 136063 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23362 grid for indexing accessible points = 1.400000 m= 61221 mr = 93791 m= 18322 mr = 47657 m= 3151 mr = 13771 m= 223 mr = 2040 m= 5 mr = 115 m= 0 mr = 2 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 627 time to turn everything in is 1.510000 number of dielectric boundary points 61609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 18221 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) : 1.729190 object centre at (A) : -2.582000 -6.751501 -21.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1275533 0.2044026 midg,1,midg; midg,igrid,midg 2.1489616E-02 0.1023083 1,midg,midg; igrid,midg,midg -4.3805670E-02 -1.0560542E-02 gauss-seidel spectral radius is 0.9991682 estimated iterations to convergence 274 setup time was (sec) 1.890000 now iterating at: 11:44:07 rms-change max change #iterations 8.475284 285.8401 at 10iterations 4.861554 127.6978 at 20iterations 2.759217 72.75336 at 30iterations 1.557750 44.14423 at 40iterations 0.8776839 22.00838 at 50iterations 0.4910180 10.72285 at 60iterations 0.2748197 6.107018 at 70iterations 0.1535857 3.120651 at 80iterations 8.5588761E-02 1.847777 at 90iterations 4.7753491E-02 0.9695721 at 100iterations 2.6575869E-02 0.6152202 at 110iterations 1.4821665E-02 0.3387070 at 120iterations 8.2422160E-03 0.1776733 at 130iterations 4.5787720E-03 0.1063474 at 140iterations 2.5493349E-03 5.8059692E-02 at 150iterations 1.4147756E-03 3.0208588E-02 at 160iterations 7.8881264E-04 1.5547752E-02 at 170iterations 4.3874621E-04 1.0038376E-02 at 180iterations finished qdiffx linear iterations at : 11:44:22 total time elapsed so far: 16.45000 # loops : 180 mean,max change (kT/e) : 4.3874621E-04 1.0038376E-02 energy calculations done at 16.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.67000 DelPhi exited at 11:44:22 16.680u 0.477s 0:17.43 98.3% 0+0k 0+0io 0pf+0w