Sun Oct 9 16:43:10 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 16:43:10 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 = 2386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6631769 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): -53.15500 -8.525000 ymin,ymax (A): 4.102000 54.90500 zmin,zma (A): -25.57000 28.11100 x,y,z range (A): 44.63000 50.80300 53.68100 scale (grids/A): 0.6631769 object centre (A): -30.84000 29.50350 1.270500 number of atom coordinates read : 2386 total number of charged atoms : 2278 net assigned charge : 1.000009 assigned positive charge : 352.0491 centred at (gu) : 90.33983 88.86177 88.64442 assigned negative charge : -351.0499 centred at (gu) : 90.41665 88.93754 88.75416 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 47701 no. pairs analyzed = 47701 no. exposed pairs = 2995 no. arc points = 21292 no. surface atoms = 1016 nbur = 1370 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3943 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.1900000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2049 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8410 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1080642E-08 -1.4379962E-08 midg,1,midg; midg,igrid,midg 2.1458847E-08 -9.7746460E-09 1,midg,midg; igrid,midg,midg 1.5906718E-08 -1.3618153E-08 gauss-seidel spectral radius is 0.9882000 estimated iterations to convergence 75 setup time was (sec) 0.3800000 now iterating at: 16:43:10 rms-change max change #iterations 0.1556330 21.59859 at 10iterations 1.6771140E-02 2.645817 at 20iterations 1.8401869E-03 0.2679691 at 30iterations 2.4189975E-04 3.5129547E-02 at 40iterations 5.1604136E-05 6.6547394E-03 at 50iterations finished qdiffx linear iterations at : 16:43:13 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 5.1604136E-05 6.6547394E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 16:43:14 3.363u 0.185s 0:03.81 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 16:43:14 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 = 2386 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: 1.989531 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): -53.15500 -8.525000 ymin,ymax (A): 4.102000 54.90500 zmin,zma (A): -25.57000 28.11100 x,y,z range (A): 44.63000 50.80300 53.68100 scale (grids/A): 1.989531 object centre (A): -30.84000 29.50350 1.270500 number of atom coordinates read : 2386 total number of charged atoms : 2278 net assigned charge : 1.000009 assigned positive charge : 352.0491 centred at (gu) : 91.01868 86.58485 85.93247 assigned negative charge : -351.0499 centred at (gu) : 91.24976 86.81244 86.26245 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21292 grid for indexing accessible points = 1.400000 m= 29023 mr = 53451 m= 5564 mr = 21572 m= 478 mr = 3581 m= 4 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3900000 number of dielectric boundary points 33597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18033 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) : 0.6631769 object centre at (A) : -30.84000 29.50350 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2782769E-02 2.4374668E-04 midg,1,midg; midg,igrid,midg -7.8907621E-04 -3.3314782E-03 1,midg,midg; igrid,midg,midg 1.4593008E-02 -2.4622625E-02 gauss-seidel spectral radius is 0.9987315 estimated iterations to convergence 222 setup time was (sec) 0.6100000 now iterating at: 16:43:14 rms-change max change #iterations 4.397352 190.0833 at 10iterations 2.120407 74.42376 at 20iterations 1.019923 31.87207 at 30iterations 0.4912198 16.77152 at 40iterations 0.2383321 8.020187 at 50iterations 0.1146228 3.738285 at 60iterations 5.5072207E-02 1.702840 at 70iterations 2.6628517E-02 0.8329135 at 80iterations 1.2840620E-02 0.3770790 at 90iterations 6.2001073E-03 0.1833115 at 100iterations 3.0035446E-03 0.1027699 at 110iterations 1.4462641E-03 4.5471191E-02 at 120iterations finished qdiffx linear iterations at : 16:43:22 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 1.4462641E-03 4.5471191E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 16:43:22 7.971u 0.205s 0:08.49 96.2% 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 16:43:22 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 = 2386 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.984296 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): -53.15500 -8.525000 ymin,ymax (A): 4.102000 54.90500 zmin,zma (A): -25.57000 28.11100 x,y,z range (A): 44.63000 50.80300 53.68100 scale (grids/A): 2.984296 object centre (A): -30.84000 29.50350 1.270500 number of atom coordinates read : 2386 total number of charged atoms : 2278 net assigned charge : 1.000009 assigned positive charge : 352.0491 centred at (gu) : 91.52799 84.87707 83.89870 assigned negative charge : -351.0499 centred at (gu) : 91.87461 85.21880 84.39372 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 178766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21292 grid for indexing accessible points = 1.400000 m= 91241 mr = 129707 m= 36138 mr = 74663 m= 10380 mr = 29207 m= 1930 mr = 7885 m= 195 mr = 1366 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 1.010000 number of dielectric boundary points 75725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18224 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) : 1.989531 object centre at (A) : -30.84000 29.50350 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2002360 0.1576566 midg,1,midg; midg,igrid,midg -6.7871049E-02 3.5802316E-02 1,midg,midg; igrid,midg,midg 0.1078645 -0.3342474 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 16:43:24 rms-change max change #iterations 10.15790 492.1323 at 10iterations 5.959856 141.1782 at 20iterations 3.486963 71.05455 at 30iterations 2.042694 42.44299 at 40iterations 1.192586 24.48066 at 50iterations 0.6950842 12.51255 at 60iterations 0.4048562 7.454433 at 70iterations 0.2354856 4.402862 at 80iterations 0.1370004 2.350214 at 90iterations 7.9508245E-02 1.377985 at 100iterations 4.6205278E-02 0.8756180 at 110iterations 2.6861046E-02 0.4896011 at 120iterations 1.5587782E-02 0.2796001 at 130iterations 9.0359114E-03 0.1577368 at 140iterations 5.2532037E-03 9.5954537E-02 at 150iterations 3.0565981E-03 5.8419228E-02 at 160iterations 1.7807328E-03 3.0157089E-02 at 170iterations 1.0423581E-03 1.7719269E-02 at 180iterations finished qdiffx linear iterations at : 16:43:35 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.0423581E-03 1.7719269E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 16:43:35 12.860u 0.202s 0:13.34 97.9% 0+0k 0+0io 0pf+0w