Sat Oct 15 11:56:15 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 Sat Oct 15 2011 at 11:56:15 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 = 2464 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5826514 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): -26.75400 26.96300 ymin,ymax (A): 43.94600 87.68200 zmin,zma (A): -13.54700 47.55300 x,y,z range (A): 53.71700 43.73600 61.10000 scale (grids/A): 0.5826514 object centre (A): 0.1045008 65.81400 17.00300 number of atom coordinates read : 2464 total number of charged atoms : 2328 net assigned charge : 10.50003 assigned positive charge : 356.8402 centred at (gu) : 90.19337 90.24610 90.09121 assigned negative charge : -346.3410 centred at (gu) : 90.19329 90.16534 90.11382 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5687 nv = 96 ne = 84 npr = 48593 no. pairs analyzed = 48593 no. exposed pairs = 3421 no. arc points = 24654 no. surface atoms = 1135 nbur = 1329 mkacc time = 9.9999994E-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 = 1.484000 m= 257 mr = 2783 m= 1 mr = 16 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 0.2600000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2449 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7112 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8757394E-09 2.1315274E-09 midg,1,midg; midg,igrid,midg 9.3645081E-10 4.2464650E-09 1,midg,midg; igrid,midg,midg 2.4046516E-09 2.6272979E-09 gauss-seidel spectral radius is 0.9847618 estimated iterations to convergence 67 setup time was (sec) 0.4800000 now iterating at: 11:56:15 rms-change max change #iterations 8.7311633E-02 14.89638 at 10iterations 6.8303435E-03 1.224147 at 20iterations 5.6363893E-04 9.6082687E-02 at 30iterations 5.8132242E-05 9.9029541E-03 at 40iterations 1.1153681E-05 2.5608540E-03 at 50iterations finished qdiffx linear iterations at : 11:56:18 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.1153681E-05 2.5608540E-03 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 11:56:18 3.080u 0.151s 0:03.51 92.0% 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 Sat Oct 15 2011 at 11:56:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2464 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: 1.747954 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): -26.75400 26.96300 ymin,ymax (A): 43.94600 87.68200 zmin,zma (A): -13.54700 47.55300 x,y,z range (A): 53.71700 43.73600 61.10000 scale (grids/A): 1.747954 object centre (A): 0.1045008 65.81400 17.00300 number of atom coordinates read : 2464 total number of charged atoms : 2328 net assigned charge : 10.50003 assigned positive charge : 356.8402 centred at (gu) : 90.57945 90.73766 90.27328 assigned negative charge : -346.3410 centred at (gu) : 90.57987 90.49606 90.34153 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 61182 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24654 grid for indexing accessible points = 1.400000 m= 20312 mr = 39916 m= 2721 mr = 13892 m= 114 mr = 1422 m= 2 mr = 19 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 0.4400000 number of dielectric boundary points 29082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18087 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) : 0.5826514 object centre at (A) : 0.1045008 65.81400 17.00300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0201083E-02 1.3919996E-02 midg,1,midg; midg,igrid,midg -4.6583889E-03 1.2792106E-02 1,midg,midg; igrid,midg,midg 2.4145912E-02 2.4177169E-02 gauss-seidel spectral radius is 0.9983838 estimated iterations to convergence 197 setup time was (sec) 0.7100000 now iterating at: 11:56:19 rms-change max change #iterations 3.349559 158.9339 at 10iterations 1.461373 61.83891 at 20iterations 0.6397558 22.93314 at 30iterations 0.2792977 10.60610 at 40iterations 0.1223344 4.225756 at 50iterations 5.3393435E-02 1.848696 at 60iterations 2.3376660E-02 0.8819580 at 70iterations 1.0241023E-02 0.3894577 at 80iterations 4.4808248E-03 0.1682339 at 90iterations 1.9631172E-03 7.1975708E-02 at 100iterations 8.6540659E-04 3.1666994E-02 at 110iterations 3.8084431E-04 1.4911175E-02 at 120iterations finished qdiffx linear iterations at : 11:56:25 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 3.8084431E-04 1.4911175E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.870000 DelPhi exited at 11:56:26 6.869u 0.176s 0:07.37 95.3% 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 15 2011 at 11:56:26 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 = 2464 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.621931 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): -26.75400 26.96300 ymin,ymax (A): 43.94600 87.68200 zmin,zma (A): -13.54700 47.55300 x,y,z range (A): 53.71700 43.73600 61.10000 scale (grids/A): 2.621931 object centre (A): 0.1045008 65.81400 17.00300 number of atom coordinates read : 2464 total number of charged atoms : 2328 net assigned charge : 10.50003 assigned positive charge : 356.8402 centred at (gu) : 90.86915 91.10638 90.40977 assigned negative charge : -346.3410 centred at (gu) : 90.86986 90.74406 90.51230 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 141725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24654 grid for indexing accessible points = 1.400000 m= 67001 mr = 97817 m= 21821 mr = 52477 m= 4493 mr = 16440 m= 516 mr = 2996 m= 17 mr = 304 m= 0 mr = 0 time to grow re-entrant surface = 0.6199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.080000 number of dielectric boundary points 65539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 18614 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) : 1.747954 object centre at (A) : 0.1045008 65.81400 17.00300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5356793 0.3300273 midg,1,midg; midg,igrid,midg -7.2888732E-02 0.1570476 1,midg,midg; igrid,midg,midg 0.3334627 0.2868991 gauss-seidel spectral radius is 0.9991947 estimated iterations to convergence 278 setup time was (sec) 1.350000 now iterating at: 11:56:27 rms-change max change #iterations 8.406249 283.3387 at 10iterations 4.827445 123.5353 at 20iterations 2.755554 75.98391 at 30iterations 1.567609 37.57828 at 40iterations 0.8871095 20.93295 at 50iterations 0.5008197 11.67557 at 60iterations 0.2824325 6.552053 at 70iterations 0.1587129 3.703804 at 80iterations 8.9455888E-02 2.008381 at 90iterations 5.0277811E-02 1.094525 at 100iterations 2.8228542E-02 0.6248417 at 110iterations 1.5866281E-02 0.3370533 at 120iterations 8.8834288E-03 0.1998997 at 130iterations 4.9936268E-03 0.1050096 at 140iterations 2.8043299E-03 5.9501648E-02 at 150iterations 1.5740816E-03 3.2657623E-02 at 160iterations 8.8293309E-04 2.0248413E-02 at 170iterations 4.9741921E-04 1.0418892E-02 at 180iterations finished qdiffx linear iterations at : 11:56:37 total time elapsed so far: 10.80000 # loops : 180 mean,max change (kT/e) : 4.9741921E-04 1.0418892E-02 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 11:56:37 10.980u 0.179s 0:11.54 96.6% 0+0k 0+0io 0pf+0w