Tue Oct 11 03:47:11 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 Tue Oct 11 2011 at 03:47:11 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: HIR 68 has a net charge of 0.5140 !!! WARNING: SEP 222 has a net charge of -0.4750 !!! WARNING: LYS 269 has a net charge of 0.2920 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6464382 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): -12.28400 36.96500 ymin,ymax (A): -27.03000 21.54800 zmin,zma (A): -9.637000 45.43400 x,y,z range (A): 49.24900 48.57800 55.07100 scale (grids/A): 0.6464382 object centre (A): 12.34050 -2.740999 17.89850 number of atom coordinates read : 2704 total number of charged atoms : 2550 net assigned charge : 3.993015 assigned positive charge : 410.5521 centred at (gu) : 90.39378 90.35578 91.79492 assigned negative charge : -406.5594 centred at (gu) : 90.16271 90.18493 91.80727 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7445 nv = 96 ne = 84 npr = 55872 no. pairs analyzed = 55872 no. exposed pairs = 3146 no. arc points = 21967 no. surface atoms = 1062 nbur = 1642 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 386 mr = 4288 m= 3 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.4000000 number of dielectric boundary points 3503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2196 ## 190 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8979 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9567751E-09 7.2140791E-09 midg,1,midg; midg,igrid,midg -1.7015973E-08 3.3577283E-08 1,midg,midg; igrid,midg,midg -2.5242347E-08 4.2948315E-08 gauss-seidel spectral radius is 0.9876029 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 03:47:12 rms-change max change #iterations 0.1583524 22.02024 at 10iterations 1.6240438E-02 2.495804 at 20iterations 1.6827370E-03 0.2353992 at 30iterations 1.7568197E-04 2.2136688E-02 at 40iterations 2.1198914E-05 2.7484894E-03 at 50iterations finished qdiffx linear iterations at : 03:47:15 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 2.1198914E-05 2.7484894E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 03:47:15 3.806u 0.215s 0:04.33 92.6% 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 03:47:15 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: HIR 68 has a net charge of 0.5140 !!! WARNING: SEP 222 has a net charge of -0.4750 !!! WARNING: LYS 269 has a net charge of 0.2920 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.939315 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): -12.28400 36.96500 ymin,ymax (A): -27.03000 21.54800 zmin,zma (A): -9.637000 45.43400 x,y,z range (A): 49.24900 48.57800 55.07100 scale (grids/A): 1.939315 object centre (A): 12.34050 -2.740999 17.89850 number of atom coordinates read : 2704 total number of charged atoms : 2550 net assigned charge : 3.993015 assigned positive charge : 410.5521 centred at (gu) : 91.18076 91.06699 95.38419 assigned negative charge : -406.5594 centred at (gu) : 90.48780 90.55447 95.42133 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 80473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21967 grid for indexing accessible points = 1.400000 m= 30101 mr = 57429 m= 4707 mr = 22808 m= 288 mr = 2949 m= 7 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1167 time to turn everything in is 0.6500000 number of dielectric boundary points 32283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20110 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) : 0.6464382 object centre at (A) : 12.34050 -2.740999 17.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1848377E-02 1.5092423E-02 midg,1,midg; midg,igrid,midg -1.6616918E-02 2.9328531E-02 1,midg,midg; igrid,midg,midg -6.7223511E-03 5.2909788E-02 gauss-seidel spectral radius is 0.9986851 estimated iterations to convergence 218 setup time was (sec) 0.9700000 now iterating at: 03:47:16 rms-change max change #iterations 4.550238 180.4965 at 10iterations 2.167889 73.88269 at 20iterations 1.029530 33.20251 at 30iterations 0.4906142 15.20609 at 40iterations 0.2330125 6.961493 at 50iterations 0.1112613 3.043011 at 60iterations 5.3088151E-02 1.619480 at 70iterations 2.5220571E-02 0.8344150 at 80iterations 1.1982132E-02 0.3737793 at 90iterations 5.7177069E-03 0.1730480 at 100iterations 2.7286811E-03 8.9862823E-02 at 110iterations 1.3037676E-03 3.9253235E-02 at 120iterations finished qdiffx linear iterations at : 03:47:24 total time elapsed so far: 8.910000 # loops : 120 mean,max change (kT/e) : 1.3037676E-03 3.9253235E-02 energy calculations done at 8.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.110000 DelPhi exited at 03:47:25 9.115u 0.268s 0:10.21 91.7% 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 03:47:25 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: 341 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2704 !!! WARNING: HIR 68 has a net charge of 0.5140 !!! WARNING: SEP 222 has a net charge of -0.4750 !!! WARNING: LYS 269 has a net charge of 0.2920 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.908972 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): -12.28400 36.96500 ymin,ymax (A): -27.03000 21.54800 zmin,zma (A): -9.637000 45.43400 x,y,z range (A): 49.24900 48.57800 55.07100 scale (grids/A): 2.908972 object centre (A): 12.34050 -2.740999 17.89850 number of atom coordinates read : 2704 total number of charged atoms : 2550 net assigned charge : 3.993015 assigned positive charge : 410.5521 centred at (gu) : 91.77115 91.60032 98.07624 assigned negative charge : -406.5594 centred at (gu) : 90.73164 90.83160 98.13187 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 185673 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21967 grid for indexing accessible points = 1.400000 m= 97648 mr = 138291 m= 35610 mr = 81420 m= 8388 mr = 28990 m= 1256 mr = 6345 m= 88 mr = 866 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 3725 time to turn everything in is 1.570000 number of dielectric boundary points 72710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 20396 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) : 1.939315 object centre at (A) : 12.34050 -2.740999 17.89850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2697541 0.3578524 midg,1,midg; midg,igrid,midg -0.1998548 0.3499890 1,midg,midg; igrid,midg,midg -3.9778661E-02 0.4538402 gauss-seidel spectral radius is 0.9992674 estimated iterations to convergence 292 setup time was (sec) 1.900000 now iterating at: 03:47:28 rms-change max change #iterations 10.49785 387.4262 at 10iterations 6.142886 139.1164 at 20iterations 3.582351 77.22826 at 30iterations 2.078884 39.66378 at 40iterations 1.208421 24.84107 at 50iterations 0.7000713 13.23760 at 60iterations 0.4053603 7.034380 at 70iterations 0.2343670 4.148720 at 80iterations 0.1357845 2.721603 at 90iterations 7.8594156E-02 1.308832 at 100iterations 4.5319963E-02 0.7500532 at 110iterations 2.6171973E-02 0.5123024 at 120iterations 1.5098479E-02 0.2660027 at 130iterations 8.7292790E-03 0.1518294 at 140iterations 5.0347680E-03 8.6509705E-02 at 150iterations 2.9065008E-03 5.4989696E-02 at 160iterations 1.6794380E-03 3.1066895E-02 at 170iterations 9.6795341E-04 1.5932083E-02 at 180iterations finished qdiffx linear iterations at : 03:47:39 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 9.6795341E-04 1.5932083E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 03:47:39 13.251u 0.265s 0:13.89 97.2% 0+0k 0+0io 0pf+0w