Wed Feb 15 08:54:21 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:21 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 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: 0.6375815 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -51.73800 1.805000 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 0.6375815 object centre (A): 38.60500 -5.237000 -24.96650 number of atom coordinates read : 2740 total number of charged atoms : 2600 net assigned charge : 4.000014 assigned positive charge : 401.6136 centred at (gu) : 90.51202 88.07978 90.42598 assigned negative charge : -397.6145 centred at (gu) : 90.40711 87.99889 90.55798 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7670 nv = 96 ne = 84 npr = 54863 no. pairs analyzed = 54863 no. exposed pairs = 3707 no. arc points = 26046 no. surface atoms = 1247 nbur = 1493 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 409 mr = 3989 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2100000 number of dielectric boundary points 4056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2494 ## 240 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8350425E-08 -1.0226183E-08 midg,1,midg; midg,igrid,midg -5.4881739E-09 9.6842374E-09 1,midg,midg; igrid,midg,midg -5.5034994E-09 1.9178961E-08 gauss-seidel spectral radius is 0.9872778 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 08:54:21 rms-change max change #iterations 0.1455332 21.70013 at 10iterations 1.4271111E-02 2.225698 at 20iterations 1.4499370E-03 0.1908855 at 30iterations 1.9012963E-04 3.1181335E-02 at 40iterations 4.4741504E-05 8.4247589E-03 at 50iterations finished qdiffx linear iterations at : 08:54:24 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 4.4741504E-05 8.4247589E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 08:54:25 3.508u 0.195s 0:04.19 88.0% 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 Wed Feb 15 2012 at 08:54:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 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: 1.912744 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -51.73800 1.805000 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 1.912744 object centre (A): 38.60500 -5.237000 -24.96650 number of atom coordinates read : 2740 total number of charged atoms : 2600 net assigned charge : 4.000014 assigned positive charge : 401.6136 centred at (gu) : 91.53540 84.23887 91.27705 assigned negative charge : -397.6145 centred at (gu) : 91.22093 83.99636 91.67366 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82251 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26046 grid for indexing accessible points = 1.400000 m= 29025 mr = 55372 m= 4233 mr = 20560 m= 224 mr = 2529 m= 5 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 0.4200000 number of dielectric boundary points 37206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20460 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) : 0.6375815 object centre at (A) : 38.60500 -5.237000 -24.96650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3563667E-02 -2.5894778E-02 midg,1,midg; midg,igrid,midg -8.2692029E-03 1.6598895E-02 1,midg,midg; igrid,midg,midg -1.5247237E-02 4.3292876E-02 gauss-seidel spectral radius is 0.9986699 estimated iterations to convergence 217 setup time was (sec) 0.7100000 now iterating at: 08:54:26 rms-change max change #iterations 4.334627 191.3503 at 10iterations 2.046727 76.65808 at 20iterations 0.9617023 32.51008 at 30iterations 0.4550234 15.82174 at 40iterations 0.2148467 6.293747 at 50iterations 0.1015359 3.528709 at 60iterations 4.8043668E-02 1.395527 at 70iterations 2.2640022E-02 0.6967912 at 80iterations 1.0708648E-02 0.3433857 at 90iterations 5.0536124E-03 0.1583061 at 100iterations 2.4023997E-03 7.0839882E-02 at 110iterations 1.1352961E-03 3.3833265E-02 at 120iterations finished qdiffx linear iterations at : 08:54:33 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 1.1352961E-03 3.3833265E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 08:54:34 8.178u 0.310s 0:08.84 95.9% 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 Wed Feb 15 2012 at 08:54:34 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2740 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: 2.869117 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): 10.68700 66.52300 ymin,ymax (A): -32.53000 22.05600 zmin,zma (A): -51.73800 1.805000 x,y,z range (A): 55.83600 54.58600 53.54300 scale (grids/A): 2.869117 object centre (A): 38.60500 -5.237000 -24.96650 number of atom coordinates read : 2740 total number of charged atoms : 2600 net assigned charge : 4.000014 assigned positive charge : 401.6136 centred at (gu) : 92.30295 81.35820 91.91564 assigned negative charge : -397.6145 centred at (gu) : 91.83128 80.99454 92.51044 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 190197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26046 grid for indexing accessible points = 1.400000 m= 94086 mr = 134854 m= 33100 mr = 75084 m= 7480 mr = 25872 m= 912 mr = 5440 m= 55 mr = 551 m= 0 mr = 25 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 1604 time to turn everything in is 1.060000 number of dielectric boundary points 84004 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 20793 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) : 1.912744 object centre at (A) : 38.60500 -5.237000 -24.96650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7140970 -0.2640183 midg,1,midg; midg,igrid,midg 8.4229916E-02 0.1550007 1,midg,midg; igrid,midg,midg -0.1071103 0.5834864 gauss-seidel spectral radius is 0.9992813 estimated iterations to convergence 294 setup time was (sec) 1.320000 now iterating at: 08:54:35 rms-change max change #iterations 10.24199 339.8529 at 10iterations 6.045934 119.0467 at 20iterations 3.547178 75.21739 at 30iterations 2.077585 45.50419 at 40iterations 1.212904 23.32957 at 50iterations 0.7045769 12.86587 at 60iterations 0.4098870 7.241398 at 70iterations 0.2381658 4.162129 at 80iterations 0.1381675 2.361084 at 90iterations 8.0145814E-02 1.382669 at 100iterations 4.6567190E-02 0.9003143 at 110iterations 2.6987381E-02 0.4980326 at 120iterations 1.5672117E-02 0.2857203 at 130iterations 9.0799099E-03 0.1602268 at 140iterations 5.2831168E-03 9.4238281E-02 at 150iterations 3.0868805E-03 5.4199219E-02 at 160iterations 1.8076008E-03 3.3309937E-02 at 170iterations 1.0740542E-03 2.0984650E-02 at 180iterations finished qdiffx linear iterations at : 08:54:50 total time elapsed so far: 15.60000 # loops : 180 mean,max change (kT/e) : 1.0740542E-03 2.0984650E-02 energy calculations done at 15.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.72000 DelPhi exited at 08:54:56 15.723u 0.234s 0:22.49 70.9% 0+0k 0+0io 0pf+0w