Mon Oct 10 14:14:03 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 Mon Oct 10 2011 at 14:14:03 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 = 2875 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5111711 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): 102.8770 172.5210 ymin,ymax (A): -11.95900 47.56600 zmin,zma (A): 34.19300 77.13100 x,y,z range (A): 69.64400 59.52500 42.93801 scale (grids/A): 0.5111711 object centre (A): 137.6990 17.80350 55.66200 number of atom coordinates read : 2875 total number of charged atoms : 2728 net assigned charge : 2.000014 assigned positive charge : 423.5356 centred at (gu) : 89.16267 93.57019 90.69502 assigned negative charge : -421.5363 centred at (gu) : 89.28381 93.55206 90.63394 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4845 nv = 96 ne = 84 npr = 56959 no. pairs analyzed = 56959 no. exposed pairs = 3695 no. arc points = 26287 no. surface atoms = 1257 nbur = 1618 mkacc time = 8.9999996E-02 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= 167 mr = 2409 m= 0 mr = 3 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 2600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2599 ## 386 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6467 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7715784E-11 1.4234390E-10 midg,1,midg; midg,igrid,midg -6.6063599E-13 1.3722076E-10 1,midg,midg; igrid,midg,midg 2.6079994E-10 -1.3134510E-10 gauss-seidel spectral radius is 0.9802950 estimated iterations to convergence 59 setup time was (sec) 0.3900000 now iterating at: 14:14:04 rms-change max change #iterations 5.1789582E-02 9.627187 at 10iterations 2.9227349E-03 0.5966530 at 20iterations 3.0516833E-04 7.4377060E-02 at 30iterations 7.5786476E-05 1.9590378E-02 at 40iterations 2.1602084E-05 5.6533813E-03 at 50iterations finished qdiffx linear iterations at : 14:14:07 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.1602084E-05 5.6533813E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 14:14:07 3.398u 0.165s 0:04.11 86.3% 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 Mon Oct 10 2011 at 14:14:07 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 = 2875 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.533513 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): 102.8770 172.5210 ymin,ymax (A): -11.95900 47.56600 zmin,zma (A): 34.19300 77.13100 x,y,z range (A): 69.64400 59.52500 42.93801 scale (grids/A): 1.533513 object centre (A): 137.6990 17.80350 55.66200 number of atom coordinates read : 2875 total number of charged atoms : 2728 net assigned charge : 2.000014 assigned positive charge : 423.5356 centred at (gu) : 87.48748 100.7099 92.08439 assigned negative charge : -421.5363 centred at (gu) : 87.85141 100.6556 91.90157 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 54034 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26287 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 16033 mr = 35771 m= 1473 mr = 10962 m= 20 mr = 633 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 24194 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 360 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 20580 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) : 0.5111711 object centre at (A) : 137.6990 17.80350 55.66200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9993805E-04 4.9180267E-03 midg,1,midg; midg,igrid,midg 3.3681463E-03 -4.9089664E-03 1,midg,midg; igrid,midg,midg 1.1447424E-04 -9.2206364E-03 gauss-seidel spectral radius is 0.9979089 estimated iterations to convergence 174 setup time was (sec) 0.5000000 now iterating at: 14:14:08 rms-change max change #iterations 2.765904 161.4199 at 10iterations 1.072146 47.07752 at 20iterations 0.4204608 16.98222 at 30iterations 0.1636807 7.148188 at 40iterations 6.3966677E-02 2.586740 at 50iterations 2.5081206E-02 1.053904 at 60iterations 9.8485667E-03 0.3919659 at 70iterations 3.8743513E-03 0.1697693 at 80iterations 1.5578243E-03 7.0647240E-02 at 90iterations 6.4980774E-04 2.5307655E-02 at 100iterations 2.9415204E-04 1.3847351E-02 at 110iterations 1.5117355E-04 7.8277588E-03 at 120iterations finished qdiffx linear iterations at : 14:14:15 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.5117355E-04 7.8277588E-03 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 14:14:16 7.551u 0.181s 0:08.13 95.0% 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 Mon Oct 10 2011 at 14:14:16 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 = 2875 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: 2.300270 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): 102.8770 172.5210 ymin,ymax (A): -11.95900 47.56600 zmin,zma (A): 34.19300 77.13100 x,y,z range (A): 69.64400 59.52500 42.93801 scale (grids/A): 2.300270 object centre (A): 137.6990 17.80350 55.66200 number of atom coordinates read : 2875 total number of charged atoms : 2728 net assigned charge : 2.000014 assigned positive charge : 423.5356 centred at (gu) : 86.23111 106.0645 93.12638 assigned negative charge : -421.5363 centred at (gu) : 86.77701 105.9835 92.85220 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 125499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26287 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 56159 mr = 87972 m= 15614 mr = 43901 m= 2217 mr = 11669 m= 116 mr = 1324 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 54723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21775 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) : 1.533513 object centre at (A) : 137.6990 17.80350 55.66200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0477317E-02 8.0230974E-02 midg,1,midg; midg,igrid,midg 5.4315947E-02 -9.0253592E-02 1,midg,midg; igrid,midg,midg -5.4258510E-02 -8.4848618E-03 gauss-seidel spectral radius is 0.9990349 estimated iterations to convergence 254 setup time was (sec) 0.9000000 now iterating at: 14:14:17 rms-change max change #iterations 7.520075 264.8413 at 10iterations 4.103967 114.7521 at 20iterations 2.212706 56.43913 at 30iterations 1.188467 27.39042 at 40iterations 0.6362417 14.52745 at 50iterations 0.3397810 7.521755 at 60iterations 0.1814349 4.032755 at 70iterations 9.6636921E-02 2.332800 at 80iterations 5.1365562E-02 1.151530 at 90iterations 2.7346855E-02 0.6450383 at 100iterations 1.4546533E-02 0.3441693 at 110iterations 7.7474616E-03 0.1806164 at 120iterations 4.1270545E-03 9.2825890E-02 at 130iterations 2.2295131E-03 5.1364899E-02 at 140iterations 1.2076311E-03 3.0384541E-02 at 150iterations 6.7503692E-04 1.6731262E-02 at 160iterations 3.9046304E-04 1.1753082E-02 at 170iterations 2.4100924E-04 7.2441101E-03 at 180iterations finished qdiffx linear iterations at : 14:14:28 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 2.4100924E-04 7.2441101E-03 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 14:14:28 11.911u 0.184s 0:12.52 96.5% 0+0k 0+0io 0pf+0w