Sat Oct 8 14:01:54 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 14:01:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6411988 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): -11.92700 43.59400 ymin,ymax (A): -22.53700 22.43100 zmin,zma (A): -2.948000 51.33500 x,y,z range (A): 55.52100 44.96800 54.28300 scale (grids/A): 0.6411988 object centre (A): 15.83350 -5.3000450E-02 24.19350 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.2786 centred at (gu) : 88.79110 89.56309 90.84216 assigned negative charge : -454.2793 centred at (gu) : 88.76952 89.45992 90.74828 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8186 nv = 96 ne = 84 npr = 64660 no. pairs analyzed = 64660 no. exposed pairs = 3420 no. arc points = 24015 no. surface atoms = 1159 nbur = 1879 mkacc time = 0.2100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 427 mr = 4779 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 3776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2290 ## 197 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 10066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1118604E-08 1.5730874E-08 midg,1,midg; midg,igrid,midg -1.6157209E-08 1.3062325E-08 1,midg,midg; igrid,midg,midg -3.9673238E-09 2.3344393E-09 gauss-seidel spectral radius is 0.9874277 estimated iterations to convergence 73 setup time was (sec) 0.7500000 now iterating at: 14:01:55 rms-change max change #iterations 0.1598039 21.25426 at 10iterations 1.6170399E-02 2.185564 at 20iterations 1.7017823E-03 0.2006073 at 30iterations 1.9561019E-04 2.9554367E-02 at 40iterations 2.6884845E-05 3.4570694E-03 at 50iterations finished qdiffx linear iterations at : 14:01:59 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 2.6884845E-05 3.4570694E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 14:02:00 4.690u 0.453s 0:05.43 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 Sat Oct 8 2011 at 14:02:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.923596 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): -11.92700 43.59400 ymin,ymax (A): -22.53700 22.43100 zmin,zma (A): -2.948000 51.33500 x,y,z range (A): 55.52100 44.96800 54.28300 scale (grids/A): 1.923596 object centre (A): 15.83350 -5.3000450E-02 24.19350 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.2786 centred at (gu) : 86.37308 88.68877 92.52594 assigned negative charge : -454.2793 centred at (gu) : 86.30820 88.37953 92.24431 start vw surface at 0.1800000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 89347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24015 grid for indexing accessible points = 1.400000 m= 32303 mr = 64673 m= 4876 mr = 24276 m= 285 mr = 3091 m= 4 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 512 time to turn everything in is 0.8900000 number of dielectric boundary points 34656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 22771 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) : 0.6411988 object centre at (A) : 15.83350 -5.3000450E-02 24.19350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4831142E-02 2.3102527E-02 midg,1,midg; midg,igrid,midg -6.7886543E-03 1.6426289E-02 1,midg,midg; igrid,midg,midg -3.2274313E-02 1.8553395E-02 gauss-seidel spectral radius is 0.9986933 estimated iterations to convergence 219 setup time was (sec) 1.240000 now iterating at: 14:02:01 rms-change max change #iterations 4.741651 192.7773 at 10iterations 2.271515 75.63393 at 20iterations 1.081642 33.50783 at 30iterations 0.5172673 15.52410 at 40iterations 0.2475717 7.024906 at 50iterations 0.1179217 3.890200 at 60iterations 5.6161791E-02 1.698887 at 70iterations 2.6837269E-02 0.7864456 at 80iterations 1.2815528E-02 0.3696952 at 90iterations 6.1353571E-03 0.1999998 at 100iterations 2.9206462E-03 7.8765869E-02 at 110iterations 1.3976985E-03 4.5646667E-02 at 120iterations finished qdiffx linear iterations at : 14:02:11 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 1.3976985E-03 4.5646667E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 14:02:11 11.027u 0.478s 0:11.79 97.4% 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 14:02:11 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.885395 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): -11.92700 43.59400 ymin,ymax (A): -22.53700 22.43100 zmin,zma (A): -2.948000 51.33500 x,y,z range (A): 55.52100 44.96800 54.28300 scale (grids/A): 2.885395 object centre (A): 15.83350 -5.3000450E-02 24.19350 number of atom coordinates read : 3038 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.2786 centred at (gu) : 84.55946 88.03289 93.78866 assigned negative charge : -454.2793 centred at (gu) : 84.46211 87.56921 93.36648 start vw surface at 0.1700000 fill in re-entrant regions at 0.7800000 boundary points on vw surface= 207194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24015 grid for indexing accessible points = 1.400000 m= 105885 mr = 156414 m= 37393 mr = 88182 m= 8831 mr = 30310 m= 1328 mr = 6676 m= 87 mr = 903 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 1718 time to turn everything in is 2.360000 number of dielectric boundary points 78190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 23122 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) : 1.923596 object centre at (A) : 15.83350 -5.3000450E-02 24.19350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1450608 0.3259698 midg,1,midg; midg,igrid,midg -2.4958767E-02 0.1768911 1,midg,midg; igrid,midg,midg -0.5496079 0.2338587 gauss-seidel spectral radius is 0.9992759 estimated iterations to convergence 293 setup time was (sec) 2.750000 now iterating at: 14:02:15 rms-change max change #iterations 10.98181 504.9863 at 10iterations 6.461948 165.5027 at 20iterations 3.778174 74.19545 at 30iterations 2.209262 43.26068 at 40iterations 1.287007 23.65824 at 50iterations 0.7485526 14.76664 at 60iterations 0.4344235 7.490339 at 70iterations 0.2529873 4.663639 at 80iterations 0.1466892 2.340622 at 90iterations 8.5022271E-02 1.406254 at 100iterations 4.9432009E-02 0.8438988 at 110iterations 2.8613374E-02 0.4550302 at 120iterations 1.6607767E-02 0.2699795 at 130iterations 9.6570263E-03 0.1551743 at 140iterations 5.6215990E-03 9.0353012E-02 at 150iterations 3.2812261E-03 5.1596642E-02 at 160iterations 1.9312687E-03 3.2163620E-02 at 170iterations 1.1487023E-03 1.9466400E-02 at 180iterations finished qdiffx linear iterations at : 14:02:31 total time elapsed so far: 18.90000 # loops : 180 mean,max change (kT/e) : 1.1487023E-03 1.9466400E-02 energy calculations done at 18.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.14000 DelPhi exited at 14:02:31 19.142u 0.506s 0:19.97 98.3% 0+0k 0+0io 0pf+0w