Tue Oct 11 07:51:32 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 Tue Oct 11 2011 at 07:51:32 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 = 2381 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: 0.6362938 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): -8.994000 36.34200 ymin,ymax (A): -14.97400 40.97500 zmin,zma (A): 5.189000 52.42600 x,y,z range (A): 45.33600 55.94900 47.23700 scale (grids/A): 0.6362938 object centre (A): 13.67400 13.00050 28.80750 number of atom coordinates read : 2381 total number of charged atoms : 2245 net assigned charge : 4.500007 assigned positive charge : 357.2813 centred at (gu) : 90.53768 88.80463 90.74400 assigned negative charge : -352.7818 centred at (gu) : 90.45652 88.80733 90.89184 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6487 nv = 96 ne = 84 npr = 48076 no. pairs analyzed = 48076 no. exposed pairs = 2881 no. arc points = 20107 no. surface atoms = 980 nbur = 1401 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 3639 m= 2 mr = 55 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 0.3200000 number of dielectric boundary points 3167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2054 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7766 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6926121E-08 -9.9680868E-09 midg,1,midg; midg,igrid,midg 7.9860607E-09 4.4546171E-09 1,midg,midg; igrid,midg,midg -1.6299538E-09 1.5317200E-08 gauss-seidel spectral radius is 0.9871832 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 07:51:33 rms-change max change #iterations 0.1359810 21.05259 at 10iterations 1.3477618E-02 1.818225 at 20iterations 1.4892165E-03 0.2322102 at 30iterations 2.1856441E-04 3.3588409E-02 at 40iterations 4.4721983E-05 6.5383911E-03 at 50iterations finished qdiffx linear iterations at : 07:51:35 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 4.4721983E-05 6.5383911E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 07:51:36 3.251u 0.199s 0:04.63 74.2% 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 Tue Oct 11 2011 at 07:51:37 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 = 2381 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: 1.908881 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): -8.994000 36.34200 ymin,ymax (A): -14.97400 40.97500 zmin,zma (A): 5.189000 52.42600 x,y,z range (A): 45.33600 55.94900 47.23700 scale (grids/A): 1.908881 object centre (A): 13.67400 13.00050 28.80750 number of atom coordinates read : 2381 total number of charged atoms : 2245 net assigned charge : 4.500007 assigned positive charge : 357.2813 centred at (gu) : 91.61264 86.41330 92.23183 assigned negative charge : -352.7818 centred at (gu) : 91.36949 86.42174 92.67533 start vw surface at 0.1700000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20107 grid for indexing accessible points = 1.400000 m= 26524 mr = 48649 m= 4333 mr = 20021 m= 247 mr = 2766 m= 4 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 29113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17609 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) : 0.6362938 object centre at (A) : 13.67400 13.00050 28.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5030518E-02 -2.2181304E-02 midg,1,midg; midg,igrid,midg 1.8027870E-02 3.3930242E-02 1,midg,midg; igrid,midg,midg -4.5486698E-03 6.6739470E-03 gauss-seidel spectral radius is 0.9986176 estimated iterations to convergence 213 setup time was (sec) 0.8200000 now iterating at: 07:51:38 rms-change max change #iterations 4.010031 167.0822 at 10iterations 1.868875 70.72523 at 20iterations 0.8785037 30.89456 at 30iterations 0.4082768 12.71745 at 40iterations 0.1921115 6.494946 at 50iterations 8.9630626E-02 2.927544 at 60iterations 4.1797344E-02 1.457703 at 70iterations 1.9548973E-02 0.6212902 at 80iterations 9.1464268E-03 0.2954025 at 90iterations 4.2918604E-03 0.1448584 at 100iterations 2.0219507E-03 7.3118210E-02 at 110iterations 9.6280436E-04 3.0950546E-02 at 120iterations finished qdiffx linear iterations at : 07:51:44 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 9.6280436E-04 3.0950546E-02 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 07:51:45 7.255u 0.200s 0:08.06 92.4% 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 Tue Oct 11 2011 at 07:51:45 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 = 2381 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: 2.863322 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): -8.994000 36.34200 ymin,ymax (A): -14.97400 40.97500 zmin,zma (A): 5.189000 52.42600 x,y,z range (A): 45.33600 55.94900 47.23700 scale (grids/A): 2.863322 object centre (A): 13.67400 13.00050 28.80750 number of atom coordinates read : 2381 total number of charged atoms : 2245 net assigned charge : 4.500007 assigned positive charge : 357.2813 centred at (gu) : 92.41882 84.61971 93.34756 assigned negative charge : -352.7818 centred at (gu) : 92.05427 84.63269 94.01297 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 160582 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20107 grid for indexing accessible points = 1.400000 m= 84674 mr = 117586 m= 31867 mr = 70018 m= 7755 mr = 25970 m= 1135 mr = 5976 m= 79 mr = 783 m= 0 mr = 46 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 65713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 17954 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) : 1.908881 object centre at (A) : 13.67400 13.00050 28.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3839211 -0.3076527 midg,1,midg; midg,igrid,midg 0.1426805 0.3612780 1,midg,midg; igrid,midg,midg -2.9158184E-02 -4.9070111E-03 gauss-seidel spectral radius is 0.9992465 estimated iterations to convergence 288 setup time was (sec) 1.560000 now iterating at: 07:51:47 rms-change max change #iterations 9.486441 295.8904 at 10iterations 5.543343 171.7592 at 20iterations 3.217068 68.37357 at 30iterations 1.857655 40.39686 at 40iterations 1.072076 21.00135 at 50iterations 0.6171769 12.18457 at 60iterations 0.3544775 7.133024 at 70iterations 0.2034050 3.979516 at 80iterations 0.1168263 2.242264 at 90iterations 6.6947296E-02 1.349986 at 100iterations 3.8402647E-02 0.8099518 at 110iterations 2.1956440E-02 0.4066086 at 120iterations 1.2584497E-02 0.2345428 at 130iterations 7.2048060E-03 0.1467962 at 140iterations 4.1281986E-03 7.8158975E-02 at 150iterations 2.3699680E-03 4.4818878E-02 at 160iterations 1.3628211E-03 2.6565552E-02 at 170iterations 7.8992464E-04 1.5342712E-02 at 180iterations finished qdiffx linear iterations at : 07:51:57 total time elapsed so far: 11.91000 # loops : 180 mean,max change (kT/e) : 7.8992464E-04 1.5342712E-02 energy calculations done at 11.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 07:51:59 12.090u 0.229s 0:13.72 89.7% 0+0k 0+0io 0pf+0w