Sun Oct 9 16:14:12 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 16:14:12 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 = 3150 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: 0.5989031 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): -15.09000 37.22100 ymin,ymax (A): -57.62400 -3.793000 zmin,zma (A): -7.164000 52.27800 x,y,z range (A): 52.31100 53.83100 59.44200 scale (grids/A): 0.5989031 object centre (A): 11.06550 -30.70850 22.55700 number of atom coordinates read : 3150 total number of charged atoms : 3006 net assigned charge : -4.499987 assigned positive charge : 467.2008 centred at (gu) : 90.16415 89.39283 91.75687 assigned negative charge : -471.7023 centred at (gu) : 90.23490 89.30791 91.80100 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7337 nv = 96 ne = 84 npr = 65390 no. pairs analyzed = 65390 no. exposed pairs = 3694 no. arc points = 26057 no. surface atoms = 1263 nbur = 1887 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 4026 m= 0 mr = 44 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2655 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9313 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5775924E-11 -5.4900946E-09 midg,1,midg; midg,igrid,midg -6.2548229E-09 1.5593550E-09 1,midg,midg; igrid,midg,midg 1.1645306E-09 -5.0123283E-09 gauss-seidel spectral radius is 0.9856150 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 16:14:12 rms-change max change #iterations 0.1215354 18.83824 at 10iterations 1.0449217E-02 1.524071 at 20iterations 9.3778450E-04 0.1331043 at 30iterations 1.5252588E-04 3.1330109E-02 at 40iterations 5.3364154E-05 1.2011528E-02 at 50iterations finished qdiffx linear iterations at : 16:14:15 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 5.3364154E-05 1.2011528E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 16:14:16 3.473u 0.175s 0:04.01 90.7% 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 16:14:16 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 = 3150 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: 1.796709 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): -15.09000 37.22100 ymin,ymax (A): -57.62400 -3.793000 zmin,zma (A): -7.164000 52.27800 x,y,z range (A): 52.31100 53.83100 59.44200 scale (grids/A): 1.796709 object centre (A): 11.06550 -30.70850 22.55700 number of atom coordinates read : 3150 total number of charged atoms : 3006 net assigned charge : -4.499987 assigned positive charge : 467.2008 centred at (gu) : 90.49160 88.17785 95.26988 assigned negative charge : -471.7023 centred at (gu) : 90.70445 87.92352 95.40270 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26057 grid for indexing accessible points = 1.400000 m= 27588 mr = 56226 m= 3943 mr = 19971 m= 152 mr = 2368 m= 0 mr = 49 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.4000000 number of dielectric boundary points 33674 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23422 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) : 0.5989031 object centre at (A) : 11.06550 -30.70850 22.55700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8541670E-03 -5.2022137E-04 midg,1,midg; midg,igrid,midg -1.9582095E-02 -1.4367271E-02 1,midg,midg; igrid,midg,midg -1.3109745E-02 -1.9628232E-02 gauss-seidel spectral radius is 0.9985169 estimated iterations to convergence 206 setup time was (sec) 0.6200000 now iterating at: 16:14:16 rms-change max change #iterations 4.221685 168.1635 at 10iterations 1.911797 61.31379 at 20iterations 0.8642502 27.21401 at 30iterations 0.3927358 12.40954 at 40iterations 0.1775738 5.637251 at 50iterations 8.0980763E-02 2.549332 at 60iterations 3.6768422E-02 1.126583 at 70iterations 1.6710790E-02 0.4937392 at 80iterations 7.6271393E-03 0.2208576 at 90iterations 3.5110691E-03 0.1116028 at 100iterations 1.6343590E-03 5.8144569E-02 at 110iterations 7.9249637E-04 2.8223991E-02 at 120iterations finished qdiffx linear iterations at : 16:14:24 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 7.9249637E-04 2.8223991E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 16:14:24 7.930u 0.202s 0:08.42 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 16:14:24 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 = 3150 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: 2.695064 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): -15.09000 37.22100 ymin,ymax (A): -57.62400 -3.793000 zmin,zma (A): -7.164000 52.27800 x,y,z range (A): 52.31100 53.83100 59.44200 scale (grids/A): 2.695064 object centre (A): 11.06550 -30.70850 22.55700 number of atom coordinates read : 3150 total number of charged atoms : 3006 net assigned charge : -4.499987 assigned positive charge : 467.2008 centred at (gu) : 90.73728 87.26681 97.90457 assigned negative charge : -471.7023 centred at (gu) : 91.05658 86.88524 98.10391 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 187404 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26057 grid for indexing accessible points = 1.400000 m= 90886 mr = 137260 m= 31294 mr = 73695 m= 6736 mr = 24741 m= 716 mr = 4954 m= 19 mr = 449 m= 0 mr = 11 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.9900000 number of dielectric boundary points 75945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 24044 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) : 1.796709 object centre at (A) : 11.06550 -30.70850 22.55700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1584740 4.9634755E-02 midg,1,midg; midg,igrid,midg -0.2072547 -0.2594814 1,midg,midg; igrid,midg,midg -0.2742459 -0.2591655 gauss-seidel spectral radius is 0.9992361 estimated iterations to convergence 286 setup time was (sec) 1.240000 now iterating at: 16:14:26 rms-change max change #iterations 10.14528 266.1301 at 10iterations 5.904952 134.7544 at 20iterations 3.411307 74.90078 at 30iterations 1.953738 40.39953 at 40iterations 1.125035 21.57379 at 50iterations 0.6451317 15.64312 at 60iterations 0.3686943 7.140167 at 70iterations 0.2110763 3.916382 at 80iterations 0.1207789 2.394279 at 90iterations 6.8896927E-02 1.354868 at 100iterations 3.9364029E-02 0.7152949 at 110iterations 2.2460841E-02 0.4497800 at 120iterations 1.2812405E-02 0.2445784 at 130iterations 7.3226620E-03 0.1329451 at 140iterations 4.1691717E-03 7.5900078E-02 at 150iterations 2.3776297E-03 4.5881271E-02 at 160iterations 1.3568209E-03 2.4624825E-02 at 170iterations 7.7360496E-04 1.4709473E-02 at 180iterations finished qdiffx linear iterations at : 16:14:37 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 7.7360496E-04 1.4709473E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.78000 DelPhi exited at 16:14:37 12.781u 0.210s 0:13.31 97.5% 0+0k 0+0io 0pf+0w