Sun Oct 9 06:37:13 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 06:37:13 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: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6731078 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): 1.949000 44.31700 ymin,ymax (A): -9.477000 38.04100 zmin,zma (A): -24.38900 28.50000 x,y,z range (A): 42.36800 47.51800 52.88900 scale (grids/A): 0.6731078 object centre (A): 23.13300 14.28200 2.055500 number of atom coordinates read : 2001 total number of charged atoms : 1856 net assigned charge : -3.068984 assigned positive charge : 300.0160 centred at (gu) : 90.01801 89.31088 88.48589 assigned negative charge : -303.0851 centred at (gu) : 89.89296 89.16103 88.47128 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6157 nv = 96 ne = 84 npr = 41683 no. pairs analyzed = 41683 no. exposed pairs = 2464 no. arc points = 17340 no. surface atoms = 835 nbur = 1166 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 351 mr = 3414 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2400000 number of dielectric boundary points 3042 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1601 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8729098E-08 -5.6645546E-09 midg,1,midg; midg,igrid,midg -4.9903619E-08 1.8053788E-08 1,midg,midg; igrid,midg,midg -3.7668737E-08 1.5818040E-08 gauss-seidel spectral radius is 0.9885034 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 06:37:14 rms-change max change #iterations 0.1570883 23.16131 at 10iterations 1.7756810E-02 2.512020 at 20iterations 1.9336321E-03 0.2636929 at 30iterations 2.1414096E-04 3.8322449E-02 at 40iterations 2.3642664E-05 3.9154291E-03 at 50iterations finished qdiffx linear iterations at : 06:37:17 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.3642664E-05 3.9154291E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 06:37:17 3.443u 0.241s 0:03.96 92.9% 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 06:37:17 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: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 2.019324 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): 1.949000 44.31700 ymin,ymax (A): -9.477000 38.04100 zmin,zma (A): -24.38900 28.50000 x,y,z range (A): 42.36800 47.51800 52.88900 scale (grids/A): 2.019324 object centre (A): 23.13300 14.28200 2.055500 number of atom coordinates read : 2001 total number of charged atoms : 1856 net assigned charge : -3.068984 assigned positive charge : 300.0160 centred at (gu) : 90.05405 87.93272 85.45757 assigned negative charge : -303.0851 centred at (gu) : 89.67882 87.48316 85.41383 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17340 grid for indexing accessible points = 1.400000 m= 24696 mr = 44520 m= 4482 mr = 18736 m= 338 mr = 2981 m= 7 mr = 156 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1280 time to turn everything in is 0.4800000 number of dielectric boundary points 27952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14691 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) : 0.6731078 object centre at (A) : 23.13300 14.28200 2.055500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9428746E-02 1.3130214E-02 midg,1,midg; midg,igrid,midg -3.4616854E-02 1.8928578E-03 1,midg,midg; igrid,midg,midg -3.0862475E-02 1.7516937E-02 gauss-seidel spectral radius is 0.9987189 estimated iterations to convergence 221 setup time was (sec) 0.7900000 now iterating at: 06:37:18 rms-change max change #iterations 4.186999 245.8386 at 10iterations 1.999717 77.18093 at 20iterations 0.9581612 33.76733 at 30iterations 0.4590516 16.03642 at 40iterations 0.2197209 7.937389 at 50iterations 0.1053242 3.984444 at 60iterations 5.0396681E-02 1.593123 at 70iterations 2.4177810E-02 0.7634163 at 80iterations 1.1589235E-02 0.3909311 at 90iterations 5.5489237E-03 0.1788979 at 100iterations 2.6650855E-03 9.6714973E-02 at 110iterations 1.2777775E-03 4.3071747E-02 at 120iterations finished qdiffx linear iterations at : 06:37:25 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.2777775E-03 4.3071747E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 06:37:26 7.793u 0.284s 0:08.35 96.6% 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 Sun Oct 9 2011 at 06:37:26 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: 337 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: SEP 59 has a net charge of -0.4750 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 3.028985 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): 1.949000 44.31700 ymin,ymax (A): -9.477000 38.04100 zmin,zma (A): -24.38900 28.50000 x,y,z range (A): 42.36800 47.51800 52.88900 scale (grids/A): 3.028985 object centre (A): 23.13300 14.28200 2.055500 number of atom coordinates read : 2001 total number of charged atoms : 1856 net assigned charge : -3.068984 assigned positive charge : 300.0160 centred at (gu) : 90.08125 86.89906 83.18638 assigned negative charge : -303.0851 centred at (gu) : 89.51834 86.22472 83.12072 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 149379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17340 grid for indexing accessible points = 1.400000 m= 77749 mr = 107453 m= 30781 mr = 64393 m= 8250 mr = 25406 m= 1446 mr = 6417 m= 129 mr = 1051 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 4529 time to turn everything in is 1.210000 number of dielectric boundary points 62948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 14848 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) : 2.019324 object centre at (A) : 23.13300 14.28200 2.055500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6264361 0.5731547 midg,1,midg; midg,igrid,midg -0.2639885 3.9987825E-02 1,midg,midg; igrid,midg,midg -0.3000080 0.1274047 gauss-seidel spectral radius is 0.9992650 estimated iterations to convergence 291 setup time was (sec) 1.540000 now iterating at: 06:37:27 rms-change max change #iterations 9.576293 444.8184 at 10iterations 5.542921 122.5023 at 20iterations 3.205545 63.95312 at 30iterations 1.851934 36.82231 at 40iterations 1.069555 23.05561 at 50iterations 0.6137918 11.76442 at 60iterations 0.3538956 7.044503 at 70iterations 0.2039643 3.784904 at 80iterations 0.1172504 2.326129 at 90iterations 6.7451037E-02 1.318027 at 100iterations 3.8768783E-02 0.6911163 at 110iterations 2.2343542E-02 0.4156704 at 120iterations 1.2849692E-02 0.2624978 at 130iterations 7.3864781E-03 0.1339768 at 140iterations 4.2358711E-03 8.0792427E-02 at 150iterations 2.4446943E-03 5.0920486E-02 at 160iterations 1.4024095E-03 2.5135040E-02 at 170iterations 8.0662197E-04 1.4211655E-02 at 180iterations finished qdiffx linear iterations at : 06:37:38 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 8.0662197E-04 1.4211655E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 06:37:39 12.725u 0.286s 0:13.28 97.8% 0+0k 0+0io 0pf+0w