Tue Oct 11 03:57:37 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 Tue Oct 11 2011 at 03:57:38 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6411065 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 0.6411065 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 0.1540153 assigned positive charge : 415.2488 centred at (gu) : 90.16376 90.28492 91.89339 assigned negative charge : -415.0953 centred at (gu) : 89.93734 90.14639 91.81842 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7375 nv = 96 ne = 84 npr = 56627 no. pairs analyzed = 56627 no. exposed pairs = 3318 no. arc points = 23152 no. surface atoms = 1109 nbur = 1628 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 4167 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3200000 number of dielectric boundary points 3573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8997 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4564096E-09 1.4412300E-08 midg,1,midg; midg,igrid,midg -1.6966668E-08 1.8576433E-08 1,midg,midg; igrid,midg,midg -2.8729037E-08 2.9308763E-08 gauss-seidel spectral radius is 0.9874012 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 03:57:38 rms-change max change #iterations 0.1569401 21.72383 at 10iterations 1.5796967E-02 2.004754 at 20iterations 1.6172187E-03 0.2236967 at 30iterations 1.6388280E-04 2.2575378E-02 at 40iterations 1.7954811E-05 2.4967194E-03 at 50iterations finished qdiffx linear iterations at : 03:57:41 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 1.7954811E-05 2.4967194E-03 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 03:57:41 3.296u 0.190s 0:03.85 90.3% 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 Tue Oct 11 2011 at 03:57:41 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.923319 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 1.923319 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 0.1540153 assigned positive charge : 415.2488 centred at (gu) : 90.49065 90.85410 95.67931 assigned negative charge : -415.0953 centred at (gu) : 89.81168 90.43887 95.45498 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 80412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23152 grid for indexing accessible points = 1.400000 m= 28918 mr = 56893 m= 4197 mr = 21436 m= 217 mr = 2557 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.5400000 number of dielectric boundary points 32792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20348 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) : 0.6411065 object centre at (A) : 12.83000 -1.701000 17.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0342219E-02 -6.1511486E-03 midg,1,midg; midg,igrid,midg -1.5501082E-02 2.2462729E-02 1,midg,midg; igrid,midg,midg -1.1455390E-02 4.7558490E-02 gauss-seidel spectral radius is 0.9986706 estimated iterations to convergence 217 setup time was (sec) 0.8300000 now iterating at: 03:57:42 rms-change max change #iterations 4.552162 193.3823 at 10iterations 2.163044 70.30873 at 20iterations 1.026146 35.01756 at 30iterations 0.4862093 15.96536 at 40iterations 0.2304045 6.970148 at 50iterations 0.1092682 3.264748 at 60iterations 5.1732749E-02 1.551214 at 70iterations 2.4577094E-02 0.6844997 at 80iterations 1.1654254E-02 0.3392522 at 90iterations 5.5241240E-03 0.1858273 at 100iterations 2.6161647E-03 8.1122398E-02 at 110iterations 1.2526863E-03 3.8495064E-02 at 120iterations finished qdiffx linear iterations at : 03:57:49 total time elapsed so far: 7.310000 # loops : 120 mean,max change (kT/e) : 1.2526863E-03 3.8495064E-02 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 03:57:49 7.491u 0.207s 0:07.98 96.3% 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 Tue Oct 11 2011 at 03:57:49 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.884979 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 2.884979 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2737 total number of charged atoms : 2585 net assigned charge : 0.1540153 assigned positive charge : 415.2488 centred at (gu) : 90.73580 91.28098 98.51874 assigned negative charge : -415.0953 centred at (gu) : 89.71761 90.65828 98.18251 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 186195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23152 grid for indexing accessible points = 1.400000 m= 94637 mr = 137918 m= 33131 mr = 77850 m= 7568 mr = 26479 m= 1049 mr = 5632 m= 50 mr = 725 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1856 time to turn everything in is 1.420000 number of dielectric boundary points 74011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 20676 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) : 1.923319 object centre at (A) : 12.83000 -1.701000 17.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5383833 0.1854042 midg,1,midg; midg,igrid,midg -0.1702235 0.2671294 1,midg,midg; igrid,midg,midg -6.9714613E-02 0.4072355 gauss-seidel spectral radius is 0.9992656 estimated iterations to convergence 291 setup time was (sec) 1.730000 now iterating at: 03:57:51 rms-change max change #iterations 10.59234 462.5511 at 10iterations 6.205440 131.2860 at 20iterations 3.627683 80.54402 at 30iterations 2.115415 54.76037 at 40iterations 1.229735 25.65785 at 50iterations 0.7130512 14.25361 at 60iterations 0.4126043 7.730244 at 70iterations 0.2394632 4.385975 at 80iterations 0.1381098 2.324280 at 90iterations 7.9902135E-02 1.462536 at 100iterations 4.6150640E-02 0.7959204 at 110iterations 2.6679995E-02 0.4740582 at 120iterations 1.5403206E-02 0.2560234 at 130iterations 8.8858642E-03 0.1732063 at 140iterations 5.1464746E-03 9.7164154E-02 at 150iterations 2.9721491E-03 5.1830053E-02 at 160iterations 1.7148219E-03 3.1613350E-02 at 170iterations 9.9624728E-04 1.9035339E-02 at 180iterations finished qdiffx linear iterations at : 03:58:02 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 9.9624728E-04 1.9035339E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 03:58:02 12.215u 0.220s 0:12.71 97.7% 0+0k 0+0io 0pf+0w