Tue Oct 11 03:47:21 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+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 Oct 11 2011 at 03:47:21 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ILE 14 has a net charge of 0.5000 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 0.6594180 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): -11.83100 36.71700 ymin,ymax (A): -26.89900 21.94600 zmin,zma (A): -8.264000 45.72300 x,y,z range (A): 48.54800 48.84500 53.98700 scale (grids/A): 0.6594180 object centre (A): 12.44300 -2.476501 18.72950 number of atom coordinates read : 2770 total number of charged atoms : 2612 net assigned charge : 3.426021 assigned positive charge : 423.9177 centred at (gu) : 90.11160 90.55753 91.51151 assigned negative charge : -420.4922 centred at (gu) : 89.93047 90.46246 91.52615 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7898 nv = 96 ne = 84 npr = 56770 no. pairs analyzed = 56770 no. exposed pairs = 3312 no. arc points = 22706 no. surface atoms = 1108 nbur = 1662 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 4498 m= 5 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2176 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9402 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5195913E-09 7.2395472E-09 midg,1,midg; midg,igrid,midg -1.0393050E-08 3.1818857E-08 1,midg,midg; igrid,midg,midg -2.9704255E-08 4.7010101E-08 gauss-seidel spectral radius is 0.9880890 estimated iterations to convergence 75 setup time was (sec) 0.6000000 now iterating at: 03:47:22 rms-change max change #iterations 0.1751938 22.58798 at 10iterations 1.8864885E-02 2.488651 at 20iterations 2.0406607E-03 0.2807236 at 30iterations 2.4500387E-04 3.0975342E-02 at 40iterations 4.2020005E-05 7.0133209E-03 at 50iterations finished qdiffx linear iterations at : 03:47:26 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 4.2020005E-05 7.0133209E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 03:47:26 4.622u 0.398s 0:05.54 90.4% 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 Oct 11 2011 at 03:47:26 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ILE 14 has a net charge of 0.5000 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 1.978254 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): -11.83100 36.71700 ymin,ymax (A): -26.89900 21.94600 zmin,zma (A): -8.264000 45.72300 x,y,z range (A): 48.54800 48.84500 53.98700 scale (grids/A): 1.978254 object centre (A): 12.44300 -2.476501 18.72950 number of atom coordinates read : 2770 total number of charged atoms : 2612 net assigned charge : 3.426021 assigned positive charge : 423.9177 centred at (gu) : 90.33412 91.67198 94.53414 assigned negative charge : -420.4922 centred at (gu) : 89.79110 91.38689 94.57821 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 84402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 32358 mr = 59601 m= 5745 mr = 24529 m= 440 mr = 3907 m= 14 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 190 time to turn everything in is 0.6900000 number of dielectric boundary points 34713 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 20613 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) : 0.6594180 object centre at (A) : 12.44300 -2.476501 18.72950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5457384E-02 1.3295148E-02 midg,1,midg; midg,igrid,midg -1.6220765E-02 -1.5374879E-02 1,midg,midg; igrid,midg,midg -4.5990888E-03 6.5884002E-02 gauss-seidel spectral radius is 0.9987422 estimated iterations to convergence 223 setup time was (sec) 1.040000 now iterating at: 03:47:28 rms-change max change #iterations 4.810553 222.7991 at 10iterations 2.322158 73.64958 at 20iterations 1.123162 34.66721 at 30iterations 0.5418217 16.50086 at 40iterations 0.2621622 7.643475 at 50iterations 0.1269734 4.261124 at 60iterations 6.1283045E-02 1.721105 at 70iterations 2.9664386E-02 0.8314838 at 80iterations 1.4335125E-02 0.4193115 at 90iterations 6.9316495E-03 0.1824837 at 100iterations 3.3480991E-03 0.1022186 at 110iterations 1.6221296E-03 4.8927307E-02 at 120iterations finished qdiffx linear iterations at : 03:47:38 total time elapsed so far: 11.18000 # loops : 120 mean,max change (kT/e) : 1.6221296E-03 4.8927307E-02 energy calculations done at 11.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.37000 DelPhi exited at 03:47:39 11.373u 0.432s 0:12.27 96.1% 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 Oct 11 2011 at 03:47:39 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 !!! WARNING: ILE 14 has a net charge of 0.5000 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 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: 2.967381 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): -11.83100 36.71700 ymin,ymax (A): -26.89900 21.94600 zmin,zma (A): -8.264000 45.72300 x,y,z range (A): 48.54800 48.84500 53.98700 scale (grids/A): 2.967381 object centre (A): 12.44300 -2.476501 18.72950 number of atom coordinates read : 2770 total number of charged atoms : 2612 net assigned charge : 3.426021 assigned positive charge : 423.9177 centred at (gu) : 90.50098 92.50767 96.80093 assigned negative charge : -420.4922 centred at (gu) : 89.68656 92.08025 96.86720 start vw surface at 0.1200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 194612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22706 grid for indexing accessible points = 1.400000 m= 102404 mr = 143561 m= 39872 mr = 84809 m= 10752 mr = 33027 m= 1927 mr = 8474 m= 188 mr = 1427 m= 9 mr = 122 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 601 time to turn everything in is 1.830000 number of dielectric boundary points 78344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 20887 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) : 1.978254 object centre at (A) : 12.44300 -2.476501 18.72950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2092752 0.3514174 midg,1,midg; midg,igrid,midg -0.1651603 -0.2602637 1,midg,midg; igrid,midg,midg -3.1611260E-02 0.5677059 gauss-seidel spectral radius is 0.9992836 estimated iterations to convergence 295 setup time was (sec) 2.170000 now iterating at: 03:47:41 rms-change max change #iterations 11.00694 415.1667 at 10iterations 6.456265 146.0316 at 20iterations 3.793897 75.65985 at 30iterations 2.220037 39.63735 at 40iterations 1.299216 24.37930 at 50iterations 0.7596687 15.54516 at 60iterations 0.4423603 8.453018 at 70iterations 0.2582394 5.709809 at 80iterations 0.1499128 2.628821 at 90iterations 8.7289162E-02 1.530729 at 100iterations 5.0836220E-02 0.8305416 at 110iterations 2.9544778E-02 0.4883385 at 120iterations 1.7195890E-02 0.2824707 at 130iterations 9.9715907E-03 0.1802382 at 140iterations 5.8218245E-03 9.8834991E-02 at 150iterations 3.3914379E-03 5.6747437E-02 at 160iterations 1.9889837E-03 3.2291412E-02 at 170iterations 1.1767392E-03 2.0729065E-02 at 180iterations finished qdiffx linear iterations at : 03:47:57 total time elapsed so far: 18.44000 # loops : 180 mean,max change (kT/e) : 1.1767392E-03 2.0729065E-02 energy calculations done at 18.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.61000 DelPhi exited at 03:47:58 18.610u 0.479s 0:19.62 97.2% 0+0k 0+0io 0pf+0w