Wed Dec 21 14:20:59 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+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 Wed Dec 21 2011 at 14:20:59 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: 236 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: 0.6401151 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): -6.221000 34.90600 ymin,ymax (A): -3.482000 48.52400 zmin,zma (A): -24.46700 31.14800 x,y,z range (A): 41.12700 52.00600 55.61500 scale (grids/A): 0.6401151 object centre (A): 14.34250 22.52100 3.340501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 90.80083 92.63037 90.16357 assigned negative charge : -285.8263 centred at (gu) : 90.91978 92.78712 90.09311 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 39612 no. pairs analyzed = 39612 no. exposed pairs = 2471 no. arc points = 17576 no. surface atoms = 834 nbur = 1130 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 324 mr = 3156 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1774 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 6570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5664704E-09 9.6947614E-09 midg,1,midg; midg,igrid,midg 9.4594741E-09 -1.8488061E-08 1,midg,midg; igrid,midg,midg 1.1297368E-08 -8.2470351E-09 gauss-seidel spectral radius is 0.9873018 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 14:21:00 rms-change max change #iterations 0.1217865 17.30063 at 10iterations 1.1935195E-02 1.947554 at 20iterations 1.1666340E-03 0.1815948 at 30iterations 1.1886862E-04 1.7865181E-02 at 40iterations 1.1399668E-05 1.7242432E-03 at 50iterations finished qdiffx linear iterations at : 14:21:04 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.1399668E-05 1.7242432E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 14:21:05 4.441u 0.292s 0:05.97 79.2% 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 Wed Dec 21 2011 at 14:21:05 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 = 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: 1.920345 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): -6.221000 34.90600 ymin,ymax (A): -3.482000 48.52400 zmin,zma (A): -24.46700 31.14800 x,y,z range (A): 41.12700 52.00600 55.61500 scale (grids/A): 1.920345 object centre (A): 14.34250 22.52100 3.340501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 92.40244 97.89113 90.49050 assigned negative charge : -285.8263 centred at (gu) : 92.75963 98.36156 90.27943 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17576 grid for indexing accessible points = 1.400000 m= 22998 mr = 41327 m= 3902 mr = 17764 m= 210 mr = 2656 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2179 time to turn everything in is 0.3400000 number of dielectric boundary points 25093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 14435 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) : 0.6401151 object centre at (A) : 14.34250 22.52100 3.340501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7572846E-02 1.1440291E-02 midg,1,midg; midg,igrid,midg 3.1191001E-02 -1.8709689E-02 1,midg,midg; igrid,midg,midg 7.0090708E-03 -4.4088606E-03 gauss-seidel spectral radius is 0.9985818 estimated iterations to convergence 210 setup time was (sec) 0.6200000 now iterating at: 14:21:06 rms-change max change #iterations 3.601732 166.4742 at 10iterations 1.664487 59.86586 at 20iterations 0.7708910 27.40979 at 30iterations 0.3571584 12.15817 at 40iterations 0.1637774 5.588844 at 50iterations 7.5602636E-02 2.660212 at 60iterations 3.4725528E-02 1.389637 at 70iterations 1.6079083E-02 0.5963192 at 80iterations 7.4142194E-03 0.2416372 at 90iterations 3.4165254E-03 0.1188245 at 100iterations 1.5765782E-03 5.1376045E-02 at 110iterations 7.3058862E-04 2.3734570E-02 at 120iterations finished qdiffx linear iterations at : 14:21:17 total time elapsed so far: 11.53000 # loops : 120 mean,max change (kT/e) : 7.3058862E-04 2.3734570E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 14:21:21 11.653u 0.406s 0:15.89 75.8% 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 Wed Dec 21 2011 at 14:21:22 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 = 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: 2.880518 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): -6.221000 34.90600 ymin,ymax (A): -3.482000 48.52400 zmin,zma (A): -24.46700 31.14800 x,y,z range (A): 41.12700 52.00600 55.61500 scale (grids/A): 2.880518 object centre (A): 14.34250 22.52100 3.340501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000005 assigned positive charge : 287.8261 centred at (gu) : 93.60358 101.8367 90.73584 assigned negative charge : -285.8263 centred at (gu) : 94.13946 102.5424 90.41917 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 138082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17576 grid for indexing accessible points = 1.400000 m= 72882 mr = 99893 m= 28318 mr = 60876 m= 7087 mr = 23627 m= 963 mr = 5629 m= 51 mr = 668 m= 0 mr = 24 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 7308 time to turn everything in is 0.8100000 number of dielectric boundary points 56666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9100000 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) : 1.920345 object centre at (A) : 14.34250 22.52100 3.340501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9691470 1.0091327E-02 midg,1,midg; midg,igrid,midg 0.3355885 -0.2017320 1,midg,midg; igrid,midg,midg 3.9630011E-02 -2.8563982E-02 gauss-seidel spectral radius is 0.9992310 estimated iterations to convergence 285 setup time was (sec) 1.080000 now iterating at: 14:21:26 rms-change max change #iterations 8.515133 351.9057 at 10iterations 4.901037 183.5973 at 20iterations 2.788655 75.34583 at 30iterations 1.589866 39.25407 at 40iterations 0.9079782 20.99523 at 50iterations 0.5159526 11.29663 at 60iterations 0.2933630 7.045486 at 70iterations 0.1666567 3.379303 at 80iterations 9.4711617E-02 1.871046 at 90iterations 5.3795151E-02 1.159261 at 100iterations 3.0465666E-02 0.6282902 at 110iterations 1.7353499E-02 0.3566933 at 120iterations 9.8353876E-03 0.2040825 at 130iterations 5.5696224E-03 0.1123848 at 140iterations 3.1636069E-03 6.7135334E-02 at 150iterations 1.7935773E-03 3.4263611E-02 at 160iterations 1.0204243E-03 2.1127701E-02 at 170iterations 5.7836616E-04 1.1474609E-02 at 180iterations finished qdiffx linear iterations at : 14:21:43 total time elapsed so far: 17.68000 # loops : 180 mean,max change (kT/e) : 5.7836616E-04 1.1474609E-02 energy calculations done at 17.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.81000 DelPhi exited at 14:21:51 17.814u 0.294s 0:28.69 63.0% 0+0k 0+0io 0pf+0w