Sun Oct 9 11:41:37 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 Sun Oct 9 2011 at 11:41:37 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: HIR 206 has a net charge of 0.5140 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: 0.6621532 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): -6.065000 47.69900 ymin,ymax (A): 8.448000 58.86500 zmin,zma (A): 5.867000 59.10900 x,y,z range (A): 53.76400 50.41700 53.24200 scale (grids/A): 0.6621532 object centre (A): 20.81700 33.65650 32.48800 number of atom coordinates read : 2771 total number of charged atoms : 2692 net assigned charge : 3.014013 assigned positive charge : 415.0500 centred at (gu) : 90.98946 90.61033 90.59252 assigned negative charge : -412.0376 centred at (gu) : 91.00275 90.57784 90.62478 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8686 nv = 96 ne = 84 npr = 52722 no. pairs analyzed = 52722 no. exposed pairs = 3931 no. arc points = 28432 no. surface atoms = 1299 nbur = 1472 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 583 mr = 4411 m= 0 mr = 108 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3100000 number of dielectric boundary points 4750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2622 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10012 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3519280E-08 1.0282876E-09 midg,1,midg; midg,igrid,midg 8.5407015E-10 1.7368144E-08 1,midg,midg; igrid,midg,midg 9.0732870E-09 6.2879519E-09 gauss-seidel spectral radius is 0.9882177 estimated iterations to convergence 75 setup time was (sec) 0.5200000 now iterating at: 11:41:37 rms-change max change #iterations 0.1712912 32.52762 at 10iterations 1.8376883E-02 2.489938 at 20iterations 1.9372213E-03 0.2558937 at 30iterations 2.1021208E-04 3.1822205E-02 at 40iterations 2.3255710E-05 3.2577515E-03 at 50iterations finished qdiffx linear iterations at : 11:41:40 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.3255710E-05 3.2577515E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 11:41:40 3.124u 0.152s 0:03.56 91.8% 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 Sun Oct 9 2011 at 11:41:40 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: HIR 206 has a net charge of 0.5140 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: 1.986459 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): -6.065000 47.69900 ymin,ymax (A): 8.448000 58.86500 zmin,zma (A): 5.867000 59.10900 x,y,z range (A): 53.76400 50.41700 53.24200 scale (grids/A): 1.986459 object centre (A): 20.81700 33.65650 32.48800 number of atom coordinates read : 2771 total number of charged atoms : 2692 net assigned charge : 3.014013 assigned positive charge : 415.0500 centred at (gu) : 92.96770 91.83031 91.77681 assigned negative charge : -412.0376 centred at (gu) : 93.00812 91.73338 91.87437 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 91978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28432 grid for indexing accessible points = 1.400000 m= 34436 mr = 60691 m= 6994 mr = 24503 m= 607 mr = 4540 m= 13 mr = 243 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 512 time to turn everything in is 0.6300000 number of dielectric boundary points 44051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 21261 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) : 0.6621532 object centre at (A) : 20.81700 33.65650 32.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4333024E-02 1.5150670E-02 midg,1,midg; midg,igrid,midg 6.2666032E-03 2.7642718E-02 1,midg,midg; igrid,midg,midg -1.8734343E-02 3.7029476E-03 gauss-seidel spectral radius is 0.9987924 estimated iterations to convergence 228 setup time was (sec) 0.8900000 now iterating at: 11:41:41 rms-change max change #iterations 4.836595 201.3108 at 10iterations 2.367760 73.93633 at 20iterations 1.153871 36.67345 at 30iterations 0.5656031 16.60991 at 40iterations 0.2768249 7.922947 at 50iterations 0.1349946 3.862581 at 60iterations 6.6156194E-02 1.956139 at 70iterations 3.2428160E-02 0.9648151 at 80iterations 1.5871834E-02 0.4844322 at 90iterations 7.7477959E-03 0.2235126 at 100iterations 3.8101953E-03 0.1172118 at 110iterations 1.8629658E-03 5.0943613E-02 at 120iterations finished qdiffx linear iterations at : 11:41:47 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.8629658E-03 5.0943613E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 11:41:48 7.105u 0.170s 0:07.58 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 Sun Oct 9 2011 at 11:41:48 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2771 !!! WARNING: HIR 206 has a net charge of 0.5140 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: 2.979689 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): -6.065000 47.69900 ymin,ymax (A): 8.448000 58.86500 zmin,zma (A): 5.867000 59.10900 x,y,z range (A): 53.76400 50.41700 53.24200 scale (grids/A): 2.979689 object centre (A): 20.81700 33.65650 32.48800 number of atom coordinates read : 2771 total number of charged atoms : 2692 net assigned charge : 3.014013 assigned positive charge : 415.0500 centred at (gu) : 94.45119 92.74513 92.66490 assigned negative charge : -412.0376 centred at (gu) : 94.51212 92.60007 92.81152 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 212477 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28432 grid for indexing accessible points = 1.400000 m= 106570 mr = 148357 m= 43461 mr = 84443 m= 13141 mr = 34486 m= 2481 mr = 9959 m= 217 mr = 1726 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.9900001 no. cavity mid-points inaccessible to solvent = 1796 time to turn everything in is 1.610000 number of dielectric boundary points 99271 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 21535 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) : 1.986459 object centre at (A) : 20.81700 33.65650 32.48800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7950341E-02 0.1965429 midg,1,midg; midg,igrid,midg 0.1158826 0.3015642 1,midg,midg; igrid,midg,midg -0.2636110 0.3487866 gauss-seidel spectral radius is 0.9993295 estimated iterations to convergence 305 setup time was (sec) 1.890000 now iterating at: 11:41:50 rms-change max change #iterations 11.28465 422.9135 at 10iterations 6.921260 179.2214 at 20iterations 4.191381 105.3956 at 30iterations 2.525382 49.78123 at 40iterations 1.520087 30.14386 at 50iterations 0.9108984 20.06629 at 60iterations 0.5439416 9.890595 at 70iterations 0.3248159 6.084305 at 80iterations 0.1930604 3.177776 at 90iterations 0.1149007 2.378657 at 100iterations 6.8189435E-02 1.183010 at 110iterations 4.0416293E-02 0.6978874 at 120iterations 2.3942349E-02 0.4155960 at 130iterations 1.4182316E-02 0.2523050 at 140iterations 8.4119616E-03 0.1373405 at 150iterations 4.9847621E-03 7.6978445E-02 at 160iterations 2.9581494E-03 4.7073364E-02 at 170iterations 1.7573251E-03 3.0654907E-02 at 180iterations finished qdiffx linear iterations at : 11:42:00 total time elapsed so far: 11.94000 # loops : 180 mean,max change (kT/e) : 1.7573251E-03 3.0654907E-02 energy calculations done at 11.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.12000 DelPhi exited at 11:42:00 12.123u 0.182s 0:12.59 97.6% 0+0k 0+0io 0pf+0w