Tue Nov 22 14:12:00 PST 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 Nov 22 2011 at 14:12:04 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6554238 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): -4.235000 34.44100 ymin,ymax (A): -3.603000 48.13700 zmin,zma (A): -23.47000 30.84600 x,y,z range (A): 38.67600 51.74000 54.31600 scale (grids/A): 0.6554238 object centre (A): 15.10300 22.26700 3.688001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 90.24253 92.71210 89.96951 assigned negative charge : -289.2262 centred at (gu) : 90.34537 92.83812 89.91162 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5758 nv = 96 ne = 84 npr = 40597 no. pairs analyzed = 40597 no. exposed pairs = 2467 no. arc points = 17183 no. surface atoms = 829 nbur = 1135 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 309 mr = 3199 m= 7 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.1500000 number of dielectric boundary points 2824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1723 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 6721 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2942302E-10 1.4616065E-08 midg,1,midg; midg,igrid,midg 1.3348339E-08 -1.7261129E-08 1,midg,midg; igrid,midg,midg 1.9433269E-08 -6.6159886E-09 gauss-seidel spectral radius is 0.9878777 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 14:12:07 rms-change max change #iterations 0.1408519 25.85293 at 10iterations 1.4393666E-02 1.931763 at 20iterations 1.5190450E-03 0.2154422 at 30iterations 1.5611255E-04 2.3501933E-02 at 40iterations 1.6360360E-05 2.4299622E-03 at 50iterations finished qdiffx linear iterations at : 14:12:18 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 1.6360360E-05 2.4299622E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.860000 DelPhi exited at 14:12:23 3.865u 0.244s 0:20.20 20.2% 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 Tue Nov 22 2011 at 14:12:25 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.966271 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): -4.235000 34.44100 ymin,ymax (A): -3.603000 48.13700 zmin,zma (A): -23.47000 30.84600 x,y,z range (A): 38.67600 51.74000 54.31600 scale (grids/A): 1.966271 object centre (A): 15.10300 22.26700 3.688001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 90.72769 98.13607 89.90842 assigned negative charge : -289.2262 centred at (gu) : 91.03625 98.51459 89.73495 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17183 grid for indexing accessible points = 1.400000 m= 22890 mr = 42570 m= 3696 mr = 17549 m= 229 mr = 2551 m= 2 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1672 time to turn everything in is 0.3300000 number of dielectric boundary points 25709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14455 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) : 0.6554238 object centre at (A) : 15.10300 22.26700 3.688001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4762442E-02 1.2952117E-02 midg,1,midg; midg,igrid,midg 4.6460766E-02 -3.5532825E-03 1,midg,midg; igrid,midg,midg 8.2944650E-03 -6.8401680E-03 gauss-seidel spectral radius is 0.9986373 estimated iterations to convergence 215 setup time was (sec) 0.5900000 now iterating at: 14:12:30 rms-change max change #iterations 3.872667 194.3040 at 10iterations 1.820887 74.49275 at 20iterations 0.8539225 30.04190 at 30iterations 0.3978086 13.40493 at 40iterations 0.1873199 6.649391 at 50iterations 8.7381326E-02 3.452835 at 60iterations 4.1100781E-02 1.415756 at 70iterations 1.9243730E-02 0.6126404 at 80iterations 8.9951092E-03 0.3267498 at 90iterations 4.2159208E-03 0.1540642 at 100iterations 1.9733433E-03 7.0210457E-02 at 110iterations 9.2234329E-04 3.0674934E-02 at 120iterations finished qdiffx linear iterations at : 14:12:54 total time elapsed so far: 8.280000 # loops : 120 mean,max change (kT/e) : 9.2234329E-04 3.0674934E-02 energy calculations done at 8.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.410000 DelPhi exited at 14:12:56 8.408u 0.285s 0:31.27 27.7% 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 Tue Nov 22 2011 at 14:12:59 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.949407 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): -4.235000 34.44100 ymin,ymax (A): -3.603000 48.13700 zmin,zma (A): -23.47000 30.84600 x,y,z range (A): 38.67600 51.74000 54.31600 scale (grids/A): 2.949407 object centre (A): 15.10300 22.26700 3.688001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 292.2259 centred at (gu) : 91.09164 102.2041 89.86275 assigned negative charge : -289.2262 centred at (gu) : 91.55444 102.7718 89.60240 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 142072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17183 grid for indexing accessible points = 1.400000 m= 73231 mr = 102843 m= 28032 mr = 60882 m= 7050 mr = 23471 m= 1105 mr = 5597 m= 67 mr = 816 m= 0 mr = 22 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 5891 time to turn everything in is 0.8300000 number of dielectric boundary points 57926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 14656 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) : 1.966271 object centre at (A) : 15.10300 22.26700 3.688001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.224375 2.2615446E-02 midg,1,midg; midg,igrid,midg 0.4896059 -0.1074165 1,midg,midg; igrid,midg,midg 4.9873620E-02 -4.5709353E-02 gauss-seidel spectral radius is 0.9992472 estimated iterations to convergence 288 setup time was (sec) 1.110000 now iterating at: 14:13:06 rms-change max change #iterations 8.957360 328.9908 at 10iterations 5.126188 114.3976 at 20iterations 2.930339 62.17408 at 30iterations 1.672760 32.53741 at 40iterations 0.9573500 19.32173 at 50iterations 0.5457085 11.13132 at 60iterations 0.3108124 6.455715 at 70iterations 0.1773009 3.740749 at 80iterations 0.1011802 2.241875 at 90iterations 5.7745870E-02 1.066971 at 100iterations 3.2858912E-02 0.6740561 at 110iterations 1.8782256E-02 0.3571506 at 120iterations 1.0697388E-02 0.2003117 at 130iterations 6.1127162E-03 0.1226473 at 140iterations 3.4890848E-03 6.6416740E-02 at 150iterations 1.9874847E-03 4.2297363E-02 at 160iterations 1.1362464E-03 2.1041870E-02 at 170iterations 6.4789358E-04 1.1939526E-02 at 180iterations finished qdiffx linear iterations at : 14:13:46 total time elapsed so far: 14.44000 # loops : 180 mean,max change (kT/e) : 6.4789358E-04 1.1939526E-02 energy calculations done at 14.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.56000 DelPhi exited at 14:13:52 14.565u 0.306s 0:52.88 28.1% 0+0k 0+0io 0pf+0w