Mon Oct 10 14:01:41 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 Mon Oct 10 2011 at 14:01:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 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: 0.6458402 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): -2.730000 46.80300 ymin,ymax (A): -16.21000 29.65700 zmin,zma (A): -18.47800 36.64400 x,y,z range (A): 49.53300 45.86700 55.12199 scale (grids/A): 0.6458402 object centre (A): 22.03650 6.723499 9.082999 number of atom coordinates read : 2312 total number of charged atoms : 2212 net assigned charge : 3.000002 assigned positive charge : 339.0192 centred at (gu) : 90.02382 88.52940 89.98244 assigned negative charge : -336.0198 centred at (gu) : 90.03155 88.62843 90.02438 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6482 nv = 96 ne = 84 npr = 47290 no. pairs analyzed = 47290 no. exposed pairs = 2807 no. arc points = 19495 no. surface atoms = 958 nbur = 1354 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 361 mr = 3661 m= 2 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2900000 number of dielectric boundary points 3108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9263664E-09 -1.3720132E-11 midg,1,midg; midg,igrid,midg 2.2665958E-08 -4.9357776E-09 1,midg,midg; igrid,midg,midg 5.8431144E-09 4.0662496E-09 gauss-seidel spectral radius is 0.9875513 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 14:01:42 rms-change max change #iterations 0.1386125 21.14607 at 10iterations 1.4101697E-02 2.064060 at 20iterations 1.4550830E-03 0.2212448 at 30iterations 1.7401759E-04 2.2993565E-02 at 40iterations 3.1079693E-05 5.8321953E-03 at 50iterations finished qdiffx linear iterations at : 14:01:46 total time elapsed so far: 4.640000 # loops : 50 mean,max change (kT/e) : 3.1079693E-05 5.8321953E-03 energy calculations done at 4.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.810000 DelPhi exited at 14:01:47 4.813u 0.373s 0:05.55 93.3% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 14:01:47 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 = 2312 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: 1.937521 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): -2.730000 46.80300 ymin,ymax (A): -16.21000 29.65700 zmin,zma (A): -18.47800 36.64400 x,y,z range (A): 49.53300 45.86700 55.12199 scale (grids/A): 1.937521 object centre (A): 22.03650 6.723499 9.082999 number of atom coordinates read : 2312 total number of charged atoms : 2212 net assigned charge : 3.000002 assigned positive charge : 339.0192 centred at (gu) : 90.07095 85.58762 89.94691 assigned negative charge : -336.0198 centred at (gu) : 90.09435 85.88519 90.07333 start vw surface at 0.1000000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19495 grid for indexing accessible points = 1.400000 m= 25926 mr = 49630 m= 4465 mr = 19346 m= 248 mr = 3005 m= 2 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 389 time to turn everything in is 0.5900000 number of dielectric boundary points 28876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17434 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) : 0.6458402 object centre at (A) : 22.03650 6.723499 9.082999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5527511E-02 1.1856871E-02 midg,1,midg; midg,igrid,midg 1.8768219E-02 -3.7501033E-03 1,midg,midg; igrid,midg,midg 5.0144943E-05 -4.1637667E-02 gauss-seidel spectral radius is 0.9986464 estimated iterations to convergence 215 setup time was (sec) 0.9000000 now iterating at: 14:01:48 rms-change max change #iterations 4.053582 176.1929 at 10iterations 1.901713 71.55226 at 20iterations 0.8897219 32.16000 at 30iterations 0.4191751 13.26914 at 40iterations 0.1962351 6.259685 at 50iterations 9.2709459E-02 2.884962 at 60iterations 4.3500945E-02 1.505085 at 70iterations 2.0427754E-02 0.6404901 at 80iterations 9.6017877E-03 0.3353806 at 90iterations 4.5477841E-03 0.1508541 at 100iterations 2.1400664E-03 6.9270134E-02 at 110iterations 1.0100715E-03 3.4439087E-02 at 120iterations finished qdiffx linear iterations at : 14:01:58 total time elapsed so far: 11.03000 # loops : 120 mean,max change (kT/e) : 1.0100715E-03 3.4439087E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.18000 DelPhi exited at 14:01:59 11.187u 0.462s 0:12.47 93.3% 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 Mon Oct 10 2011 at 14:02:02 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 = 2312 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: 2.906281 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): -2.730000 46.80300 ymin,ymax (A): -16.21000 29.65700 zmin,zma (A): -18.47800 36.64400 x,y,z range (A): 49.53300 45.86700 55.12199 scale (grids/A): 2.906281 object centre (A): 22.03650 6.723499 9.082999 number of atom coordinates read : 2312 total number of charged atoms : 2212 net assigned charge : 3.000002 assigned positive charge : 339.0192 centred at (gu) : 90.10633 83.38134 89.92019 assigned negative charge : -336.0198 centred at (gu) : 90.14146 83.82776 90.10993 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 162725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19495 grid for indexing accessible points = 1.400000 m= 82819 mr = 120097 m= 31254 mr = 68312 m= 8139 mr = 25541 m= 1180 mr = 6350 m= 61 mr = 816 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1294 time to turn everything in is 1.520000 number of dielectric boundary points 65039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 17695 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) : 1.937521 object centre at (A) : 22.03650 6.723499 9.082999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2273729 0.1069863 midg,1,midg; midg,igrid,midg 0.1146815 -5.5689972E-02 1,midg,midg; igrid,midg,midg 1.5407100E-02 -0.6334524 gauss-seidel spectral radius is 0.9992543 estimated iterations to convergence 289 setup time was (sec) 1.850000 now iterating at: 14:02:05 rms-change max change #iterations 9.476446 440.3160 at 10iterations 5.533324 136.2089 at 20iterations 3.209002 62.28946 at 30iterations 1.857976 37.11615 at 40iterations 1.078284 20.52301 at 50iterations 0.6215620 12.50280 at 60iterations 0.3583022 7.772431 at 70iterations 0.2061334 4.537270 at 80iterations 0.1188658 2.209000 at 90iterations 6.8264320E-02 1.285206 at 100iterations 3.9322305E-02 0.7665939 at 110iterations 2.2581572E-02 0.4158783 at 120iterations 1.2969378E-02 0.2642860 at 130iterations 7.4519943E-03 0.1473846 at 140iterations 4.2840303E-03 7.0304871E-02 at 150iterations 2.4603379E-03 4.4878960E-02 at 160iterations 1.4189717E-03 2.7023315E-02 at 170iterations 8.2092627E-04 1.5860319E-02 at 180iterations finished qdiffx linear iterations at : 14:02:21 total time elapsed so far: 18.19000 # loops : 180 mean,max change (kT/e) : 8.2092627E-04 1.5860319E-02 energy calculations done at 18.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.36000 DelPhi exited at 14:02:23 18.369u 0.457s 0:20.04 93.8% 0+0k 0+0io 0pf+0w