Sun Oct 9 06:05:51 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 Sun Oct 9 2011 at 06:05:51 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6338806 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): 11.81100 67.97300 ymin,ymax (A): -26.21700 26.72400 zmin,zma (A): -5.303000 37.19100 x,y,z range (A): 56.16200 52.94100 42.49400 scale (grids/A): 0.6338806 object centre (A): 39.89200 0.2534990 15.94400 number of atom coordinates read : 2124 total number of charged atoms : 1979 net assigned charge : -11.09999 assigned positive charge : 324.9645 centred at (gu) : 90.29135 89.44087 90.36321 assigned negative charge : -336.0649 centred at (gu) : 90.33909 89.17336 90.13699 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5860 nv = 96 ne = 84 npr = 41579 no. pairs analyzed = 41579 no. exposed pairs = 2994 no. arc points = 21396 no. surface atoms = 1006 nbur = 1118 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 274 mr = 2839 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2600000 number of dielectric boundary points 3282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2099 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6902 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0695119E-08 5.9538054E-09 midg,1,midg; midg,igrid,midg -4.1668880E-08 7.6880129E-09 1,midg,midg; igrid,midg,midg -8.8057410E-09 -1.8601048E-08 gauss-seidel spectral radius is 0.9870775 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 06:05:52 rms-change max change #iterations 0.1270600 22.24287 at 10iterations 1.2428317E-02 1.768488 at 20iterations 1.2519775E-03 0.1996975 at 30iterations 1.6468919E-04 3.4595490E-02 at 40iterations 3.2161821E-05 7.4806213E-03 at 50iterations finished qdiffx linear iterations at : 06:05:56 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 3.2161821E-05 7.4806213E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 06:05:56 4.120u 0.220s 0:04.67 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 06:05:56 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 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: 1.901642 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): 11.81100 67.97300 ymin,ymax (A): -26.21700 26.72400 zmin,zma (A): -5.303000 37.19100 x,y,z range (A): 56.16200 52.94100 42.49400 scale (grids/A): 1.901642 object centre (A): 39.89200 0.2534990 15.94400 number of atom coordinates read : 2124 total number of charged atoms : 1979 net assigned charge : -11.09999 assigned positive charge : 324.9645 centred at (gu) : 90.87386 88.32214 91.08927 assigned negative charge : -336.0649 centred at (gu) : 91.01715 87.52009 90.41093 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 62516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21396 grid for indexing accessible points = 1.400000 m= 20598 mr = 40015 m= 2984 mr = 14298 m= 158 mr = 1662 m= 6 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 706 time to turn everything in is 0.5600000 number of dielectric boundary points 30241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15548 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) : 0.6338806 object centre at (A) : 39.89200 0.2534990 15.94400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3178672E-02 1.6578842E-03 midg,1,midg; midg,igrid,midg -6.6021606E-02 3.8458060E-02 1,midg,midg; igrid,midg,midg -5.7297405E-02 -7.4739650E-02 gauss-seidel spectral radius is 0.9985958 estimated iterations to convergence 212 setup time was (sec) 0.8800000 now iterating at: 06:05:57 rms-change max change #iterations 3.900584 188.1129 at 10iterations 1.795731 69.35999 at 20iterations 0.8307582 30.55304 at 30iterations 0.3805896 13.66155 at 40iterations 0.1769402 6.313123 at 50iterations 8.1437342E-02 2.776417 at 60iterations 3.7528083E-02 1.317970 at 70iterations 1.7451031E-02 0.6136310 at 80iterations 8.1264526E-03 0.2834996 at 90iterations 3.8188256E-03 0.1352520 at 100iterations 1.8340164E-03 7.7816010E-02 at 110iterations 9.0810278E-04 3.3826828E-02 at 120iterations finished qdiffx linear iterations at : 06:06:05 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 9.0810278E-04 3.3826828E-02 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 06:06:06 9.274u 0.262s 0:09.87 96.5% 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 06:06:06 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2124 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.852463 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): 11.81100 67.97300 ymin,ymax (A): -26.21700 26.72400 zmin,zma (A): -5.303000 37.19100 x,y,z range (A): 56.16200 52.94100 42.49400 scale (grids/A): 2.852463 object centre (A): 39.89200 0.2534990 15.94400 number of atom coordinates read : 2124 total number of charged atoms : 1979 net assigned charge : -11.09999 assigned positive charge : 324.9645 centred at (gu) : 91.31071 87.48323 91.63385 assigned negative charge : -336.0649 centred at (gu) : 91.52568 86.28012 90.61621 start vw surface at 0.1500000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 144411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21396 grid for indexing accessible points = 1.400000 m= 67407 mr = 97977 m= 22941 mr = 52842 m= 5052 mr = 17560 m= 698 mr = 3528 m= 35 mr = 422 m= 0 mr = 7 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 2321 time to turn everything in is 1.300000 number of dielectric boundary points 68208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 15832 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) : 1.901642 object centre at (A) : 39.89200 0.2534990 15.94400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3298011 -1.4603265E-02 midg,1,midg; midg,igrid,midg -0.8391578 0.3736816 1,midg,midg; igrid,midg,midg -1.063717 -1.263249 gauss-seidel spectral radius is 0.9992491 estimated iterations to convergence 288 setup time was (sec) 1.630000 now iterating at: 06:06:08 rms-change max change #iterations 9.275266 563.6063 at 10iterations 5.413639 134.7040 at 20iterations 3.135354 71.34885 at 30iterations 1.811256 47.08789 at 40iterations 1.040121 22.99309 at 50iterations 0.5972269 12.34050 at 60iterations 0.3424420 7.154734 at 70iterations 0.1963052 4.018274 at 80iterations 0.1123687 2.262520 at 90iterations 6.4403012E-02 1.262327 at 100iterations 3.6905125E-02 0.7354069 at 110iterations 2.1181352E-02 0.4566460 at 120iterations 1.2186609E-02 0.2507839 at 130iterations 7.0291129E-03 0.1439749 at 140iterations 4.1155368E-03 9.4402313E-02 at 150iterations 2.4654567E-03 5.8498383E-02 at 160iterations 1.5271133E-03 3.6886215E-02 at 170iterations 9.9258218E-04 2.4904251E-02 at 180iterations finished qdiffx linear iterations at : 06:06:21 total time elapsed so far: 14.71000 # loops : 180 mean,max change (kT/e) : 9.9258218E-04 2.4904251E-02 energy calculations done at 14.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 06:06:21 14.888u 0.257s 0:15.43 98.0% 0+0k 0+0io 0pf+0w