Tue Oct 11 05:58:15 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 Tue Oct 11 2011 at 05:58:15 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7381757 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): -18.02100 30.20600 ymin,ymax (A): -11.63200 30.50700 zmin,zma (A): -8.649000 38.11800 x,y,z range (A): 48.22700 42.13900 46.76700 scale (grids/A): 0.7381757 object centre (A): 6.092501 9.437500 14.73450 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.500009 assigned positive charge : 314.9840 centred at (gu) : 90.08826 89.76122 91.02345 assigned negative charge : -308.4842 centred at (gu) : 90.02608 89.67360 90.90697 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7757 nv = 96 ne = 84 npr = 41683 no. pairs analyzed = 41683 no. exposed pairs = 2488 no. arc points = 17131 no. surface atoms = 849 nbur = 1224 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 548 mr = 4557 m= 1 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2800000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1520 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3454918E-10 2.6373843E-07 midg,1,midg; midg,igrid,midg 2.6635847E-08 1.8272836E-07 1,midg,midg; igrid,midg,midg 4.9363969E-08 1.7009270E-07 gauss-seidel spectral radius is 0.9904255 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 05:58:15 rms-change max change #iterations 0.2406830 30.27851 at 10iterations 3.2701612E-02 4.072024 at 20iterations 4.6392656E-03 0.5648575 at 30iterations 7.4799667E-04 9.7953796E-02 at 40iterations 1.6124260E-04 1.9512177E-02 at 50iterations finished qdiffx linear iterations at : 05:58:18 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.6124260E-04 1.9512177E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 05:58:19 3.374u 0.149s 0:03.81 92.1% 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 05:58:19 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 = 2073 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: 2.214527 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): -18.02100 30.20600 ymin,ymax (A): -11.63200 30.50700 zmin,zma (A): -8.649000 38.11800 x,y,z range (A): 48.22700 42.13900 46.76700 scale (grids/A): 2.214527 object centre (A): 6.092501 9.437500 14.73450 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.500009 assigned positive charge : 314.9840 centred at (gu) : 90.26457 89.28382 93.07018 assigned negative charge : -308.4842 centred at (gu) : 90.07836 89.02094 92.72092 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17131 grid for indexing accessible points = 1.400000 m= 34786 mr = 58253 m= 7474 mr = 27016 m= 810 mr = 5213 m= 40 mr = 480 m= 0 mr = 16 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 216 time to turn everything in is 0.6400000 number of dielectric boundary points 33398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15492 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) : 0.7381757 object centre at (A) : 6.092501 9.437500 14.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4614222E-02 4.8309140E-02 midg,1,midg; midg,igrid,midg 2.9051358E-02 2.9956799E-02 1,midg,midg; igrid,midg,midg 5.0185904E-02 3.5775874E-02 gauss-seidel spectral radius is 0.9989107 estimated iterations to convergence 240 setup time was (sec) 0.9200000 now iterating at: 05:58:20 rms-change max change #iterations 4.945514 178.8525 at 10iterations 2.506847 85.39378 at 20iterations 1.276765 39.17302 at 30iterations 0.6484440 17.85509 at 40iterations 0.3296345 9.670520 at 50iterations 0.1683319 4.823802 at 60iterations 8.5317940E-02 2.483169 at 70iterations 4.3716982E-02 1.257965 at 80iterations 2.2308504E-02 0.7010841 at 90iterations 1.1433491E-02 0.3499832 at 100iterations 5.8725490E-03 0.1991472 at 110iterations 3.0628582E-03 8.5998535E-02 at 120iterations finished qdiffx linear iterations at : 05:58:26 total time elapsed so far: 7.440000 # loops : 120 mean,max change (kT/e) : 3.0628582E-03 8.5998535E-02 energy calculations done at 7.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 05:58:27 7.646u 0.170s 0:08.25 94.6% 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 05:58:27 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 = 2073 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.321791 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): -18.02100 30.20600 ymin,ymax (A): -11.63200 30.50700 zmin,zma (A): -8.649000 38.11800 x,y,z range (A): 48.22700 42.13900 46.76700 scale (grids/A): 3.321791 object centre (A): 6.092501 9.437500 14.73450 number of atom coordinates read : 2073 total number of charged atoms : 1945 net assigned charge : 6.500009 assigned positive charge : 314.9840 centred at (gu) : 90.39690 88.92568 94.60523 assigned negative charge : -308.4842 centred at (gu) : 90.11749 88.53140 94.08147 start vw surface at 0.1400000 fill in re-entrant regions at 0.9400000 boundary points on vw surface= 186782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17131 grid for indexing accessible points = 1.400000 m= 105836 mr = 139484 m= 46494 mr = 89227 m= 14483 mr = 38942 m= 3285 mr = 11587 m= 539 mr = 2456 m= 56 mr = 381 m= 1 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 2.100000 number of dielectric boundary points 75362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 15560 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) : 2.214527 object centre at (A) : 6.092501 9.437500 14.73450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5082294 0.4348115 midg,1,midg; midg,igrid,midg 0.2522102 0.1635146 1,midg,midg; igrid,midg,midg 0.3148586 0.1653982 gauss-seidel spectral radius is 0.9993163 estimated iterations to convergence 302 setup time was (sec) 2.420000 now iterating at: 05:58:29 rms-change max change #iterations 10.79467 306.2500 at 10iterations 6.443200 136.8043 at 20iterations 3.833432 78.38242 at 30iterations 2.280393 42.86521 at 40iterations 1.354770 25.73523 at 50iterations 0.8001198 15.27657 at 60iterations 0.4740108 8.925316 at 70iterations 0.2805612 5.274673 at 80iterations 0.1659038 2.880960 at 90iterations 9.7996213E-02 1.757915 at 100iterations 5.7885997E-02 0.9610176 at 110iterations 3.4372333E-02 0.5585541 at 120iterations 2.0484427E-02 0.3834305 at 130iterations 1.2377426E-02 0.1971970 at 140iterations 7.6237069E-03 0.1361847 at 150iterations 4.8703165E-03 8.7854385E-02 at 160iterations 3.2460568E-03 6.5502167E-02 at 170iterations 2.3140071E-03 4.1740417E-02 at 180iterations finished qdiffx linear iterations at : 05:58:40 total time elapsed so far: 13.17000 # loops : 180 mean,max change (kT/e) : 2.3140071E-03 4.1740417E-02 energy calculations done at 13.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 05:58:41 13.377u 0.217s 0:13.98 97.1% 0+0k 0+0io 0pf+0w