Sat Oct 8 19:41:43 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 Sat Oct 8 2011 at 19:41:43 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6165890 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): -10.67200 38.80200 ymin,ymax (A): -22.57900 25.57600 zmin,zma (A): -12.46600 45.27100 x,y,z range (A): 49.47400 48.15500 57.73700 scale (grids/A): 0.6165890 object centre (A): 14.06500 1.498500 16.40250 number of atom coordinates read : 2576 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 88.53040 89.15425 89.56147 assigned negative charge : -386.5045 centred at (gu) : 88.43467 89.20479 89.44717 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6368 nv = 96 ne = 84 npr = 53679 no. pairs analyzed = 53679 no. exposed pairs = 3029 no. arc points = 21786 no. surface atoms = 1015 nbur = 1561 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 345 mr = 3516 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 66 time to turn everything in is 0.2000000 number of dielectric boundary points 3164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2161 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7971 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7394240E-09 8.5068974E-09 midg,1,midg; midg,igrid,midg 6.7994068E-09 -3.0859848E-10 1,midg,midg; igrid,midg,midg -4.4554849E-09 6.0017578E-09 gauss-seidel spectral radius is 0.9863735 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 19:41:43 rms-change max change #iterations 0.1190294 19.02191 at 10iterations 1.0764290E-02 1.420212 at 20iterations 9.8322029E-04 0.1484642 at 30iterations 9.0467285E-05 1.2504578E-02 at 40iterations 8.1399421E-06 1.2731552E-03 at 50iterations finished qdiffx linear iterations at : 19:41:46 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 8.1399421E-06 1.2731552E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 19:41:47 3.545u 0.185s 0:03.99 93.2% 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 Sat Oct 8 2011 at 19:41:47 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.849767 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): -10.67200 38.80200 ymin,ymax (A): -22.57900 25.57600 zmin,zma (A): -12.46600 45.27100 x,y,z range (A): 49.47400 48.15500 57.73700 scale (grids/A): 1.849767 object centre (A): 14.06500 1.498500 16.40250 number of atom coordinates read : 2576 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 85.59071 87.46242 88.68407 assigned negative charge : -386.5045 centred at (gu) : 85.30347 87.61431 88.34117 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21786 grid for indexing accessible points = 1.400000 m= 23982 mr = 48219 m= 3373 mr = 17558 m= 168 mr = 2033 m= 0 mr = 37 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4031 time to turn everything in is 0.3400000 number of dielectric boundary points 29034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 19216 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) : 0.6165890 object centre at (A) : 14.06500 1.498500 16.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5754506E-03 2.4382487E-02 midg,1,midg; midg,igrid,midg 9.1102934E-03 1.3502906E-03 1,midg,midg; igrid,midg,midg -3.1450349E-03 3.1431731E-02 gauss-seidel spectral radius is 0.9985492 estimated iterations to convergence 208 setup time was (sec) 0.5600000 now iterating at: 19:41:48 rms-change max change #iterations 3.944780 166.6841 at 10iterations 1.802343 62.23770 at 20iterations 0.8230501 26.77354 at 30iterations 0.3761079 12.77119 at 40iterations 0.1723297 5.503708 at 50iterations 7.9120114E-02 2.585445 at 60iterations 3.6130555E-02 1.257162 at 70iterations 1.6476355E-02 0.5327353 at 80iterations 7.5857062E-03 0.2581406 at 90iterations 3.4592270E-03 0.1112785 at 100iterations 1.5842235E-03 4.9051285E-02 at 110iterations 7.2568754E-04 2.3902893E-02 at 120iterations finished qdiffx linear iterations at : 19:41:55 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 7.2568754E-04 2.3902893E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 19:41:55 8.120u 0.236s 0:08.63 96.7% 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 Sat Oct 8 2011 at 19:41:56 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 = 2576 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.774651 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): -10.67200 38.80200 ymin,ymax (A): -22.57900 25.57600 zmin,zma (A): -12.46600 45.27100 x,y,z range (A): 49.47400 48.15500 57.73700 scale (grids/A): 2.774651 object centre (A): 14.06500 1.498500 16.40250 number of atom coordinates read : 2576 total number of charged atoms : 2453 net assigned charge : 3.500004 assigned positive charge : 390.0040 centred at (gu) : 83.38596 86.19363 88.02587 assigned negative charge : -386.5045 centred at (gu) : 82.95525 86.42147 87.51164 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160710 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21786 grid for indexing accessible points = 1.400000 m= 79050 mr = 116910 m= 26672 mr = 64695 m= 5931 mr = 21323 m= 716 mr = 4290 m= 36 mr = 437 m= 0 mr = 11 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 13419 time to turn everything in is 0.8800000 number of dielectric boundary points 65449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19620 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) : 1.849767 object centre at (A) : 14.06500 1.498500 16.40250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3323708E-02 0.2958177 midg,1,midg; midg,igrid,midg 0.1187398 2.5617264E-02 1,midg,midg; igrid,midg,midg -3.4315992E-02 0.4294724 gauss-seidel spectral radius is 0.9992290 estimated iterations to convergence 284 setup time was (sec) 1.130000 now iterating at: 19:41:57 rms-change max change #iterations 9.319043 302.8029 at 10iterations 5.346843 122.4694 at 20iterations 3.047562 69.37566 at 30iterations 1.735241 41.47752 at 40iterations 0.9876784 22.48311 at 50iterations 0.5613983 11.78091 at 60iterations 0.3192868 6.621843 at 70iterations 0.1813030 4.034433 at 80iterations 0.1030952 1.851103 at 90iterations 5.8535282E-02 1.070545 at 100iterations 3.3212043E-02 0.7933655 at 110iterations 1.8853258E-02 0.3595314 at 120iterations 1.0698430E-02 0.2022600 at 130iterations 6.0664243E-03 0.1207175 at 140iterations 3.4425091E-03 6.4479828E-02 at 150iterations 1.9521643E-03 3.6491752E-02 at 160iterations 1.1079703E-03 2.0727634E-02 at 170iterations 6.2697427E-04 1.2620449E-02 at 180iterations finished qdiffx linear iterations at : 19:42:09 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 6.2697427E-04 1.2620449E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 19:42:09 13.150u 0.247s 0:13.66 98.0% 0+0k 0+0io 0pf+0w