Sat Oct 15 13:19:51 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 15 2011 at 13:19:52 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 = 3164 !!! WARNING: GLU 255 has a net charge of -0.2720 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: 0.5611690 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): 8.805000 59.40600 ymin,ymax (A): -31.45600 31.98300 zmin,zma (A): 44.66800 95.74500 x,y,z range (A): 50.60100 63.43900 51.07700 scale (grids/A): 0.5611690 object centre (A): 34.10550 0.2635002 70.20650 number of atom coordinates read : 3164 total number of charged atoms : 3019 net assigned charge : 0.2280074 assigned positive charge : 476.6289 centred at (gu) : 89.79407 90.57865 91.21660 assigned negative charge : -476.4022 centred at (gu) : 89.85403 90.56685 91.09727 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6467 nv = 96 ne = 84 npr = 62542 no. pairs analyzed = 62542 no. exposed pairs = 4132 no. arc points = 29281 no. surface atoms = 1377 nbur = 1787 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 257 mr = 3260 m= 0 mr = 10 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3100000 number of dielectric boundary points 3454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2958 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1095873E-09 1.9686577E-09 midg,1,midg; midg,igrid,midg -1.2360765E-10 1.7197159E-10 1,midg,midg; igrid,midg,midg 7.7779450E-10 -7.0653133E-10 gauss-seidel spectral radius is 0.9836388 estimated iterations to convergence 64 setup time was (sec) 0.5600000 now iterating at: 13:19:52 rms-change max change #iterations 8.2021967E-02 15.35201 at 10iterations 5.9230444E-03 0.9293594 at 20iterations 4.4834430E-04 7.5229645E-02 at 30iterations 4.4997672E-05 6.8397522E-03 at 40iterations 8.0548434E-06 1.1997223E-03 at 50iterations finished qdiffx linear iterations at : 13:19:55 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 8.0548434E-06 1.1997223E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 13:19:56 3.422u 0.212s 0:04.12 88.1% 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 Sat Oct 15 2011 at 13:19:56 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 = 3164 !!! WARNING: GLU 255 has a net charge of -0.2720 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: 1.683507 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): 8.805000 59.40600 ymin,ymax (A): -31.45600 31.98300 zmin,zma (A): 44.66800 95.74500 x,y,z range (A): 50.60100 63.43900 51.07700 scale (grids/A): 1.683507 object centre (A): 34.10550 0.2635002 70.20650 number of atom coordinates read : 3164 total number of charged atoms : 3019 net assigned charge : 0.2280074 assigned positive charge : 476.6289 centred at (gu) : 89.38144 91.73506 93.64886 assigned negative charge : -476.4022 centred at (gu) : 89.56160 91.70039 93.29156 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 71579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29281 grid for indexing accessible points = 1.400000 m= 21941 mr = 47652 m= 2264 mr = 14898 m= 75 mr = 1092 m= 0 mr = 7 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1461 time to turn everything in is 0.5200000 number of dielectric boundary points 32210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 23213 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) : 0.5611690 object centre at (A) : 34.10550 0.2635002 70.20650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8026795E-03 4.0237987E-03 midg,1,midg; midg,igrid,midg 3.2076731E-04 3.5929272E-03 1,midg,midg; igrid,midg,midg 8.9527350E-03 5.0955019E-03 gauss-seidel spectral radius is 0.9983293 estimated iterations to convergence 194 setup time was (sec) 0.8200000 now iterating at: 13:19:57 rms-change max change #iterations 3.647508 157.5415 at 10iterations 1.577306 62.23697 at 20iterations 0.6751548 22.64359 at 30iterations 0.2925757 10.14178 at 40iterations 0.1261381 4.498192 at 50iterations 5.4362636E-02 1.941643 at 60iterations 2.3481840E-02 0.7774086 at 70iterations 1.0126807E-02 0.3584423 at 80iterations 4.3798746E-03 0.1373291 at 90iterations 1.8968876E-03 6.8283081E-02 at 100iterations 8.2284893E-04 3.0530691E-02 at 110iterations 3.5570475E-04 1.1526108E-02 at 120iterations finished qdiffx linear iterations at : 13:20:03 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 3.5570475E-04 1.1526108E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 13:20:04 7.766u 0.243s 0:08.32 96.1% 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 Sat Oct 15 2011 at 13:20:04 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 = 3164 !!! WARNING: GLU 255 has a net charge of -0.2720 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: 2.525260 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): 8.805000 59.40600 ymin,ymax (A): -31.45600 31.98300 zmin,zma (A): 44.66800 95.74500 x,y,z range (A): 50.60100 63.43900 51.07700 scale (grids/A): 2.525260 object centre (A): 34.10550 0.2635002 70.20650 number of atom coordinates read : 3164 total number of charged atoms : 3019 net assigned charge : 0.2280074 assigned positive charge : 476.6289 centred at (gu) : 89.07219 92.60252 95.47318 assigned negative charge : -476.4022 centred at (gu) : 89.34239 92.55044 94.93732 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 166359 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29281 grid for indexing accessible points = 1.400000 m= 75326 mr = 116759 m= 21617 mr = 59342 m= 3528 mr = 15972 m= 282 mr = 2210 m= 1 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 4703 time to turn everything in is 1.240000 number of dielectric boundary points 72672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 24137 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) : 1.683507 object centre at (A) : 34.10550 0.2635002 70.20650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7580957E-03 7.7759996E-02 midg,1,midg; midg,igrid,midg -0.1223406 0.1475942 1,midg,midg; igrid,midg,midg 0.1314559 9.7433612E-02 gauss-seidel spectral radius is 0.9991949 estimated iterations to convergence 278 setup time was (sec) 1.560000 now iterating at: 13:20:06 rms-change max change #iterations 9.428379 311.5766 at 10iterations 5.450826 135.2068 at 20iterations 3.130261 67.96229 at 30iterations 1.788620 48.53584 at 40iterations 1.019354 21.63837 at 50iterations 0.5783817 12.38494 at 60iterations 0.3276277 6.921532 at 70iterations 0.1853283 4.571560 at 80iterations 0.1044304 2.271091 at 90iterations 5.8986370E-02 1.340178 at 100iterations 3.3211149E-02 0.6663780 at 110iterations 1.8716626E-02 0.3947744 at 120iterations 1.0503785E-02 0.2182541 at 130iterations 5.9124115E-03 0.1209742 at 140iterations 3.3205510E-03 6.8815053E-02 at 150iterations 1.8673387E-03 4.1301310E-02 at 160iterations 1.0478717E-03 2.1226883E-02 at 170iterations 5.8935414E-04 1.2543678E-02 at 180iterations finished qdiffx linear iterations at : 13:20:17 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 5.8935414E-04 1.2543678E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 13:20:17 12.603u 0.246s 0:13.33 96.3% 0+0k 0+0io 0pf+0w