Tue Oct 11 07:58:48 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 07:58:48 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 = 2376 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: 0.6263856 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): -57.20600 -0.3720000 ymin,ymax (A): -38.15100 5.277000 zmin,zma (A): -20.18000 23.93200 x,y,z range (A): 56.83400 43.42800 44.11200 scale (grids/A): 0.6263856 object centre (A): -28.78900 -16.43700 1.875999 number of atom coordinates read : 2376 total number of charged atoms : 2239 net assigned charge : 4.500007 assigned positive charge : 356.7223 centred at (gu) : 89.97987 89.30452 89.59149 assigned negative charge : -352.2228 centred at (gu) : 90.03889 89.17710 89.62625 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6190 nv = 96 ne = 84 npr = 48085 no. pairs analyzed = 48085 no. exposed pairs = 2858 no. arc points = 20346 no. surface atoms = 960 nbur = 1416 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 3442 m= 0 mr = 35 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1995 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6120106E-09 1.7848134E-09 midg,1,midg; midg,igrid,midg -5.7718275E-09 1.1658631E-08 1,midg,midg; igrid,midg,midg 8.7474632E-09 1.5750801E-10 gauss-seidel spectral radius is 0.9867775 estimated iterations to convergence 71 setup time was (sec) 0.3800000 now iterating at: 07:58:49 rms-change max change #iterations 0.1242241 16.24634 at 10iterations 1.1891941E-02 1.814602 at 20iterations 1.1494949E-03 0.1813641 at 30iterations 1.0762802E-04 1.6170502E-02 at 40iterations 1.0117539E-05 1.4500618E-03 at 50iterations finished qdiffx linear iterations at : 07:58:52 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.0117539E-05 1.4500618E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 07:58:52 3.412u 0.170s 0:04.08 87.7% 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 07:58:52 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 = 2376 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: 1.879157 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): -57.20600 -0.3720000 ymin,ymax (A): -38.15100 5.277000 zmin,zma (A): -20.18000 23.93200 x,y,z range (A): 56.83400 43.42800 44.11200 scale (grids/A): 1.879157 object centre (A): -28.78900 -16.43700 1.875999 number of atom coordinates read : 2376 total number of charged atoms : 2239 net assigned charge : 4.500007 assigned positive charge : 356.7223 centred at (gu) : 89.93918 87.91326 88.77422 assigned negative charge : -352.2228 centred at (gu) : 90.11662 87.53125 88.87864 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 67555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20346 grid for indexing accessible points = 1.400000 m= 23238 mr = 47381 m= 3281 mr = 17266 m= 169 mr = 1918 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 430 time to turn everything in is 0.3200000 number of dielectric boundary points 27631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 17557 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) : 0.6263856 object centre at (A) : -28.78900 -16.43700 1.875999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6780352E-02 8.4211435E-03 midg,1,midg; midg,igrid,midg -1.8898005E-02 9.6106920E-03 1,midg,midg; igrid,midg,midg 4.5594428E-02 2.7862867E-02 gauss-seidel spectral radius is 0.9985754 estimated iterations to convergence 210 setup time was (sec) 0.5500000 now iterating at: 07:58:53 rms-change max change #iterations 3.870787 153.7579 at 10iterations 1.791529 63.12761 at 20iterations 0.8267695 31.35704 at 30iterations 0.3821074 12.76442 at 40iterations 0.1755292 5.611529 at 50iterations 8.1313446E-02 2.918308 at 60iterations 3.7523955E-02 1.230143 at 70iterations 1.7312301E-02 0.6269665 at 80iterations 7.9489099E-03 0.2711449 at 90iterations 3.6783144E-03 0.1352005 at 100iterations 1.6969140E-03 5.6747437E-02 at 110iterations 7.8266894E-04 2.5512695E-02 at 120iterations finished qdiffx linear iterations at : 07:59:00 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 7.8266894E-04 2.5512695E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 07:59:01 7.817u 0.202s 0:08.46 94.6% 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 07:59:01 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 = 2376 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: 2.818735 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): -57.20600 -0.3720000 ymin,ymax (A): -38.15100 5.277000 zmin,zma (A): -20.18000 23.93200 x,y,z range (A): 56.83400 43.42800 44.11200 scale (grids/A): 2.818735 object centre (A): -28.78900 -16.43700 1.875999 number of atom coordinates read : 2376 total number of charged atoms : 2239 net assigned charge : 4.500007 assigned positive charge : 356.7223 centred at (gu) : 89.90860 86.86987 88.16135 assigned negative charge : -352.2228 centred at (gu) : 90.17480 86.29688 88.31799 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 156549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20346 grid for indexing accessible points = 1.400000 m= 77899 mr = 114887 m= 25966 mr = 64324 m= 5592 mr = 20685 m= 729 mr = 4084 m= 47 mr = 509 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1582 time to turn everything in is 0.8300000 number of dielectric boundary points 62276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 17908 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) : 1.879157 object centre at (A) : -28.78900 -16.43700 1.875999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1873854 0.1178410 midg,1,midg; midg,igrid,midg -0.2658859 8.9593761E-02 1,midg,midg; igrid,midg,midg 0.5779358 0.3024809 gauss-seidel spectral radius is 0.9992336 estimated iterations to convergence 285 setup time was (sec) 1.070000 now iterating at: 07:59:02 rms-change max change #iterations 9.062347 375.5290 at 10iterations 5.198764 119.7324 at 20iterations 2.974687 60.05018 at 30iterations 1.702201 33.10653 at 40iterations 0.9696626 17.83959 at 50iterations 0.5531314 10.56173 at 60iterations 0.3145486 6.167526 at 70iterations 0.1791517 3.451015 at 80iterations 0.1019238 2.213621 at 90iterations 5.7836104E-02 1.093905 at 100iterations 3.2887302E-02 0.6280518 at 110iterations 1.8704593E-02 0.3594589 at 120iterations 1.0654895E-02 0.2108650 at 130iterations 6.0541527E-03 0.1185369 at 140iterations 3.4506919E-03 6.4682007E-02 at 150iterations 1.9612238E-03 3.5135269E-02 at 160iterations 1.1225946E-03 2.1537781E-02 at 170iterations 6.4129016E-04 1.2207031E-02 at 180iterations finished qdiffx linear iterations at : 07:59:13 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 6.4129016E-04 1.2207031E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 07:59:14 12.187u 0.200s 0:13.39 92.4% 0+0k 0+0io 0pf+0w