Sat Oct 15 11:28:18 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 15 2011 at 11:28:18 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3243 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: 0.5576004 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): -7.295000 44.04900 ymin,ymax (A): -38.47900 25.36600 zmin,zma (A): -15.26000 33.56000 x,y,z range (A): 51.34400 63.84500 48.82000 scale (grids/A): 0.5576004 object centre (A): 18.37700 -6.556499 9.149999 number of atom coordinates read : 3243 total number of charged atoms : 3098 net assigned charge : -1.499992 assigned positive charge : 482.9678 centred at (gu) : 88.80673 91.71947 90.51339 assigned negative charge : -484.4691 centred at (gu) : 88.86514 91.67527 90.46838 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6510 nv = 96 ne = 84 npr = 66366 no. pairs analyzed = 66366 no. exposed pairs = 4042 no. arc points = 27687 no. surface atoms = 1366 nbur = 1877 mkacc time = 0.1100000 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 = 1.540000 m= 267 mr = 3495 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2792 ## 337 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8657662E-10 3.7345482E-10 midg,1,midg; midg,igrid,midg -4.3254600E-10 4.9477283E-10 1,midg,midg; igrid,midg,midg 6.4043776E-10 -6.0924882E-10 gauss-seidel spectral radius is 0.9834274 estimated iterations to convergence 64 setup time was (sec) 0.4400000 now iterating at: 11:28:19 rms-change max change #iterations 8.4681116E-02 12.17425 at 10iterations 5.9826644E-03 0.9565582 at 20iterations 4.6481745E-04 6.8099976E-02 at 30iterations 5.1673389E-05 7.0877075E-03 at 40iterations 1.0787805E-05 1.6846657E-03 at 50iterations finished qdiffx linear iterations at : 11:28:24 total time elapsed so far: 3.610000 # loops : 50 mean,max change (kT/e) : 1.0787805E-05 1.6846657E-03 energy calculations done at 3.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 11:28:25 3.746u 0.202s 0:06.37 61.8% 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 Sat Oct 15 2011 at 11:28:25 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3243 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: 1.672801 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): -7.295000 44.04900 ymin,ymax (A): -38.47900 25.36600 zmin,zma (A): -15.26000 33.56000 x,y,z range (A): 51.34400 63.84500 48.82000 scale (grids/A): 1.672801 object centre (A): 18.37700 -6.556499 9.149999 number of atom coordinates read : 3243 total number of charged atoms : 3098 net assigned charge : -1.499992 assigned positive charge : 482.9678 centred at (gu) : 86.41936 95.15742 91.53941 assigned negative charge : -484.4691 centred at (gu) : 86.59516 95.02541 91.40494 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27687 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23191 mr = 50500 m= 2475 mr = 16139 m= 86 mr = 1247 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 499 time to turn everything in is 0.3700000 number of dielectric boundary points 30512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 282 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23859 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) : 0.5576004 object centre at (A) : 18.37700 -6.556499 9.149999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7586270E-03 3.1388996E-03 midg,1,midg; midg,igrid,midg 1.0561522E-02 3.5487874E-03 1,midg,midg; igrid,midg,midg 7.5672478E-03 -7.8266468E-03 gauss-seidel spectral radius is 0.9982908 estimated iterations to convergence 192 setup time was (sec) 0.6200000 now iterating at: 11:28:25 rms-change max change #iterations 3.659273 152.8878 at 10iterations 1.561040 67.40301 at 20iterations 0.6702858 24.47510 at 30iterations 0.2867149 10.05276 at 40iterations 0.1226081 4.027641 at 50iterations 5.2700162E-02 1.823040 at 60iterations 2.2489494E-02 0.7145367 at 70iterations 9.6633276E-03 0.3718596 at 80iterations 4.1539879E-03 0.1558247 at 90iterations 1.7838501E-03 5.5824280E-02 at 100iterations 7.6679769E-04 2.5720596E-02 at 110iterations 3.3241464E-04 1.1052370E-02 at 120iterations finished qdiffx linear iterations at : 11:28:34 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 3.3241464E-04 1.1052370E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 11:28:35 9.448u 0.264s 0:10.05 96.5% 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 15 2011 at 11:28:35 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3243 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: 2.509202 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): -7.295000 44.04900 ymin,ymax (A): -38.47900 25.36600 zmin,zma (A): -15.26000 33.56000 x,y,z range (A): 51.34400 63.84500 48.82000 scale (grids/A): 2.509202 object centre (A): 18.37700 -6.556499 9.149999 number of atom coordinates read : 3243 total number of charged atoms : 3098 net assigned charge : -1.499992 assigned positive charge : 482.9678 centred at (gu) : 84.62892 97.73593 92.30896 assigned negative charge : -484.4691 centred at (gu) : 84.89259 97.53809 92.10750 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 168691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27687 grid for indexing accessible points = 1.400000 m= 80355 mr = 123087 m= 23204 mr = 64493 m= 3976 mr = 17487 m= 338 mr = 2657 m= 11 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1731 time to turn everything in is 0.9200000 number of dielectric boundary points 68708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 24753 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) : 1.672801 object centre at (A) : 18.37700 -6.556499 9.149999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1345137 6.5894902E-02 midg,1,midg; midg,igrid,midg 0.3447905 -2.5223274E-02 1,midg,midg; igrid,midg,midg 0.1284966 -9.1636673E-02 gauss-seidel spectral radius is 0.9991703 estimated iterations to convergence 274 setup time was (sec) 1.190000 now iterating at: 11:28:36 rms-change max change #iterations 9.349692 328.8211 at 10iterations 5.296278 126.1572 at 20iterations 3.000641 66.11307 at 30iterations 1.693193 37.08982 at 40iterations 0.9486601 21.51419 at 50iterations 0.5311395 11.34851 at 60iterations 0.2972599 6.436089 at 70iterations 0.1661855 3.487385 at 80iterations 9.2831664E-02 1.767056 at 90iterations 5.1759291E-02 0.9832191 at 100iterations 2.8858736E-02 0.5425429 at 110iterations 1.6091982E-02 0.2940960 at 120iterations 8.9581488E-03 0.1767759 at 130iterations 4.9812798E-03 0.1053992 at 140iterations 2.7741489E-03 5.5297732E-02 at 150iterations 1.5485495E-03 2.9403210E-02 at 160iterations 8.6410000E-04 1.6022682E-02 at 170iterations 4.8171516E-04 1.0540009E-02 at 180iterations finished qdiffx linear iterations at : 11:28:49 total time elapsed so far: 14.17000 # loops : 180 mean,max change (kT/e) : 4.8171516E-04 1.0540009E-02 energy calculations done at 14.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.29000 DelPhi exited at 11:28:50 14.296u 0.270s 0:15.11 96.3% 0+0k 0+0io 0pf+0w