Wed Dec 28 11:01:56 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 Wed Dec 28 2011 at 11:01:56 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6446939 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): -5.999000 34.52800 ymin,ymax (A): -3.678000 47.89600 zmin,zma (A): -24.27100 30.94900 x,y,z range (A): 40.52700 51.57400 55.22000 scale (grids/A): 0.6446939 object centre (A): 14.26450 22.10900 3.339001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.4260 centred at (gu) : 90.76099 92.59594 90.14985 assigned negative charge : -289.4262 centred at (gu) : 90.88484 92.74813 90.08862 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5510 nv = 96 ne = 84 npr = 41181 no. pairs analyzed = 41181 no. exposed pairs = 2410 no. arc points = 16873 no. surface atoms = 818 nbur = 1146 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 260 mr = 3094 m= 0 mr = 33 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2643 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1725 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 6594 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1026549E-09 1.0122835E-08 midg,1,midg; midg,igrid,midg 1.0693052E-08 -2.0197493E-08 1,midg,midg; igrid,midg,midg 1.3441393E-08 -9.9849382E-09 gauss-seidel spectral radius is 0.9874749 estimated iterations to convergence 73 setup time was (sec) 0.6400000 now iterating at: 11:01:57 rms-change max change #iterations 0.1304484 19.25606 at 10iterations 1.3055208E-02 2.191593 at 20iterations 1.3222743E-03 0.2141895 at 30iterations 1.3226837E-04 2.2338867E-02 at 40iterations 1.3140785E-05 2.1140575E-03 at 50iterations finished qdiffx linear iterations at : 11:02:02 total time elapsed so far: 5.150000 # loops : 50 mean,max change (kT/e) : 1.3140785E-05 2.1140575E-03 energy calculations done at 5.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 11:02:04 5.351u 0.402s 0:07.85 73.2% 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 28 2011 at 11:02:05 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: 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.934082 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): -5.999000 34.52800 ymin,ymax (A): -3.678000 47.89600 zmin,zma (A): -24.27100 30.94900 x,y,z range (A): 40.52700 51.57400 55.22000 scale (grids/A): 1.934082 object centre (A): 14.26450 22.10900 3.339001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.4260 centred at (gu) : 92.28305 97.78781 90.44950 assigned negative charge : -289.4262 centred at (gu) : 92.65472 98.24468 90.26603 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16873 grid for indexing accessible points = 1.400000 m= 21549 mr = 41442 m= 3139 mr = 16300 m= 140 mr = 1941 m= 4 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1239 time to turn everything in is 0.5800000 number of dielectric boundary points 24666 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.7300000 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) : 0.6446939 object centre at (A) : 14.26450 22.10900 3.339001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9934203E-02 1.1634310E-02 midg,1,midg; midg,igrid,midg 3.0304648E-02 -1.7580945E-02 1,midg,midg; igrid,midg,midg 9.8576695E-03 -7.0978170E-03 gauss-seidel spectral radius is 0.9985945 estimated iterations to convergence 211 setup time was (sec) 0.8900000 now iterating at: 11:02:06 rms-change max change #iterations 3.693623 179.2138 at 10iterations 1.712016 64.46466 at 20iterations 0.7927526 29.46245 at 30iterations 0.3690494 13.99257 at 40iterations 0.1701237 5.971461 at 50iterations 7.8740060E-02 2.840373 at 60iterations 3.6463775E-02 1.472271 at 70iterations 1.6929759E-02 0.6662903 at 80iterations 7.8221774E-03 0.2770367 at 90iterations 3.6203363E-03 0.1283302 at 100iterations 1.6793701E-03 5.7137489E-02 at 110iterations 7.7838800E-04 2.8624773E-02 at 120iterations finished qdiffx linear iterations at : 11:02:15 total time elapsed so far: 10.01000 # loops : 120 mean,max change (kT/e) : 7.7838800E-04 2.8624773E-02 energy calculations done at 10.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.20000 DelPhi exited at 11:02:17 10.205u 0.432s 0:12.55 84.7% 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 Wed Dec 28 2011 at 11:02:18 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.901123 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): -5.999000 34.52800 ymin,ymax (A): -3.678000 47.89600 zmin,zma (A): -24.27100 30.94900 x,y,z range (A): 40.52700 51.57400 55.22000 scale (grids/A): 2.901123 object centre (A): 14.26450 22.10900 3.339001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.4260 centred at (gu) : 93.42445 101.6817 90.67416 assigned negative charge : -289.4262 centred at (gu) : 93.98210 102.3670 90.39899 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 137687 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16873 grid for indexing accessible points = 1.400000 m= 70227 mr = 100206 m= 25037 mr = 58245 m= 5438 mr = 20593 m= 614 mr = 4007 m= 28 mr = 353 m= 2 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4199 time to turn everything in is 1.480000 number of dielectric boundary points 55626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 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) : 1.934082 object centre at (A) : 14.26450 22.10900 3.339001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9467463 -3.7009381E-03 midg,1,midg; midg,igrid,midg 0.3065561 -0.1790828 1,midg,midg; igrid,midg,midg 5.4888628E-02 -4.3511387E-02 gauss-seidel spectral radius is 0.9992316 estimated iterations to convergence 285 setup time was (sec) 1.900000 now iterating at: 11:02:20 rms-change max change #iterations 8.710102 419.4703 at 10iterations 5.000615 121.6859 at 20iterations 2.849427 66.69080 at 30iterations 1.616226 35.81530 at 40iterations 0.9229388 17.99920 at 50iterations 0.5234647 10.26783 at 60iterations 0.2975940 6.526700 at 70iterations 0.1692617 3.562252 at 80iterations 9.5913231E-02 1.990564 at 90iterations 5.4599758E-02 1.220706 at 100iterations 3.0965365E-02 0.6352348 at 110iterations 1.7515309E-02 0.3650799 at 120iterations 9.9645900E-03 0.1935081 at 130iterations 5.6447089E-03 0.1058569 at 140iterations 3.2065220E-03 6.2231064E-02 at 150iterations 1.8235277E-03 3.5647392E-02 at 160iterations 1.0343556E-03 2.0864487E-02 at 170iterations 5.8667682E-04 1.1461258E-02 at 180iterations finished qdiffx linear iterations at : 11:02:39 total time elapsed so far: 19.97000 # loops : 180 mean,max change (kT/e) : 5.8667682E-04 1.1461258E-02 energy calculations done at 19.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.15000 DelPhi exited at 11:02:40 20.154u 0.584s 0:22.11 93.7% 0+0k 0+0io 0pf+0w