Mon Oct 10 21:35:41 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 21:35:41 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5237759 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): -11.24500 56.72300 ymin,ymax (A): 27.01000 91.99700 zmin,zma (A): -12.09200 43.91200 x,y,z range (A): 67.96800 64.98700 56.00400 scale (grids/A): 0.5237759 object centre (A): 22.73900 59.50350 15.91000 number of atom coordinates read : 3239 total number of charged atoms : 3096 net assigned charge : -4.499975 assigned positive charge : 490.2007 centred at (gu) : 87.87239 88.81942 90.60025 assigned negative charge : -494.7023 centred at (gu) : 87.88728 88.76559 90.70330 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 5575 nv = 96 ne = 84 npr = 63517 no. pairs analyzed = 63517 no. exposed pairs = 4910 no. arc points = 34056 no. surface atoms = 1613 nbur = 1626 mkacc time = 0.1800000 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 = 1.624000 m= 218 mr = 2241 m= 0 mr = 6 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3349 ## 427 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 7514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7447792E-10 -5.0400661E-10 midg,1,midg; midg,igrid,midg -3.7489345E-10 4.0054540E-11 1,midg,midg; igrid,midg,midg -1.0593536E-10 -9.1117489E-11 gauss-seidel spectral radius is 0.9812560 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 21:35:42 rms-change max change #iterations 6.2029377E-02 11.57067 at 10iterations 3.6657746E-03 0.6664174 at 20iterations 2.8914766E-04 5.5751801E-02 at 30iterations 5.6643890E-05 1.2529373E-02 at 40iterations 1.5045780E-05 3.2997131E-03 at 50iterations finished qdiffx linear iterations at : 21:35:45 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 1.5045780E-05 3.2997131E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 21:35:46 4.081u 0.175s 0:04.88 87.0% 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 21:35:46 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.571328 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): -11.24500 56.72300 ymin,ymax (A): 27.01000 91.99700 zmin,zma (A): -12.09200 43.91200 x,y,z range (A): 67.96800 64.98700 56.00400 scale (grids/A): 1.571328 object centre (A): 22.73900 59.50350 15.91000 number of atom coordinates read : 3239 total number of charged atoms : 3096 net assigned charge : -4.499975 assigned positive charge : 490.2007 centred at (gu) : 83.61641 86.45729 91.79945 assigned negative charge : -494.7023 centred at (gu) : 83.66164 86.29655 92.10971 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 60619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34056 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 17364 mr = 35880 m= 1791 mr = 10229 m= 48 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 32994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 364 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23435 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) : 0.5237759 object centre at (A) : 22.73900 59.50350 15.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1501747E-03 -1.6590942E-02 midg,1,midg; midg,igrid,midg 3.9948053E-03 7.1494970E-03 1,midg,midg; igrid,midg,midg 5.6276796E-04 -8.0313478E-03 gauss-seidel spectral radius is 0.9980713 estimated iterations to convergence 181 setup time was (sec) 1.000000 now iterating at: 21:35:47 rms-change max change #iterations 3.202397 173.4113 at 10iterations 1.287760 51.92733 at 20iterations 0.5180270 18.80715 at 30iterations 0.2104286 9.396683 at 40iterations 8.4809855E-02 3.766863 at 50iterations 3.4341160E-02 1.378170 at 60iterations 1.3865554E-02 0.5289612 at 70iterations 5.6220694E-03 0.2082624 at 80iterations 2.2945353E-03 9.6431732E-02 at 90iterations 9.4780320E-04 4.0819228E-02 at 100iterations 3.9869113E-04 1.4648438E-02 at 110iterations 1.7335752E-04 6.7582130E-03 at 120iterations finished qdiffx linear iterations at : 21:35:56 total time elapsed so far: 9.520000 # loops : 120 mean,max change (kT/e) : 1.7335752E-04 6.7582130E-03 energy calculations done at 9.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.750000 DelPhi exited at 21:35:56 9.753u 0.278s 0:10.43 96.0% 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 21:35:56 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3239 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.356992 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): -11.24500 56.72300 ymin,ymax (A): 27.01000 91.99700 zmin,zma (A): -12.09200 43.91200 x,y,z range (A): 67.96800 64.98700 56.00400 scale (grids/A): 2.356992 object centre (A): 22.73900 59.50350 15.91000 number of atom coordinates read : 3239 total number of charged atoms : 3096 net assigned charge : -4.499975 assigned positive charge : 490.2007 centred at (gu) : 80.42440 84.68581 92.69895 assigned negative charge : -494.7023 centred at (gu) : 80.49230 84.44462 93.16452 start vw surface at 0.2100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 140604 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34056 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 58571 mr = 89817 m= 17068 mr = 41706 m= 2720 mr = 11603 m= 160 mr = 1554 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.460000 number of dielectric boundary points 74405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 24731 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) : 1.571328 object centre at (A) : 22.73900 59.50350 15.91000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7088996E-02 -0.2029577 midg,1,midg; midg,igrid,midg 0.1324934 0.1193012 1,midg,midg; igrid,midg,midg 3.9772019E-02 -0.1205923 gauss-seidel spectral radius is 0.9991143 estimated iterations to convergence 265 setup time was (sec) 1.850000 now iterating at: 21:35:58 rms-change max change #iterations 8.831529 292.6373 at 10iterations 5.030414 163.2452 at 20iterations 2.835440 73.76488 at 30iterations 1.581002 46.20615 at 40iterations 0.8752969 21.02673 at 50iterations 0.4833846 11.26881 at 60iterations 0.2667523 6.126186 at 70iterations 0.1461506 3.601320 at 80iterations 8.0359124E-02 1.868323 at 90iterations 4.3952130E-02 0.9868765 at 100iterations 2.4029411E-02 0.6602859 at 110iterations 1.3128160E-02 0.3043923 at 120iterations 7.1892114E-03 0.1986885 at 130iterations 3.9259619E-03 8.3695412E-02 at 140iterations 2.1559249E-03 5.0004959E-02 at 150iterations 1.1858144E-03 2.5750160E-02 at 160iterations 6.5634522E-04 1.4739990E-02 at 170iterations 3.6778679E-04 8.8825226E-03 at 180iterations finished qdiffx linear iterations at : 21:36:12 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 3.6778679E-04 8.8825226E-03 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.77000 DelPhi exited at 21:36:13 15.767u 0.302s 0:16.56 96.9% 0+0k 0+0io 0pf+0w