Sat Oct 8 11:36:49 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 Sat Oct 8 2011 at 11:36:49 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 !!! WARNING: HIR 14 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6245066 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): 35.22300 92.22800 ymin,ymax (A): 33.85500 84.43500 zmin,zma (A): 20.75400 69.76800 x,y,z range (A): 57.00500 50.58000 49.01400 scale (grids/A): 0.6245066 object centre (A): 63.72550 59.14500 45.26100 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -5.485964 assigned positive charge : 511.3104 centred at (gu) : 90.21783 89.97957 89.29962 assigned negative charge : -516.7974 centred at (gu) : 90.13943 90.14735 89.29865 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8222 nv = 96 ne = 84 npr = 72358 no. pairs analyzed = 72358 no. exposed pairs = 3721 no. arc points = 25168 no. surface atoms = 1268 nbur = 2088 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 4839 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 86 time to turn everything in is 0.3700000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2525 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10515 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9942891E-09 -4.2883106E-09 midg,1,midg; midg,igrid,midg 1.1587565E-08 -2.2201114E-08 1,midg,midg; igrid,midg,midg -1.2434070E-08 2.9186522E-09 gauss-seidel spectral radius is 0.9867689 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 11:36:50 rms-change max change #iterations 0.1558392 19.65794 at 10iterations 1.4548525E-02 2.130835 at 20iterations 1.3443520E-03 0.1601686 at 30iterations 1.2971296E-04 1.7040253E-02 at 40iterations 1.2227011E-05 1.4839172E-03 at 50iterations finished qdiffx linear iterations at : 11:36:53 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.2227011E-05 1.4839172E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 11:36:53 3.480u 0.173s 0:04.05 90.1% 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 Sat Oct 8 2011 at 11:36:53 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 !!! WARNING: HIR 14 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.873520 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): 35.22300 92.22800 ymin,ymax (A): 33.85500 84.43500 zmin,zma (A): 20.75400 69.76800 x,y,z range (A): 57.00500 50.58000 49.01400 scale (grids/A): 1.873520 object centre (A): 63.72550 59.14500 45.26100 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -5.485964 assigned positive charge : 511.3104 centred at (gu) : 90.65252 89.93767 87.89775 assigned negative charge : -516.7974 centred at (gu) : 90.41776 90.44155 87.89526 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 90013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25168 grid for indexing accessible points = 1.400000 m= 32862 mr = 65162 m= 5110 mr = 25334 m= 284 mr = 3352 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2877 time to turn everything in is 0.6700000 number of dielectric boundary points 34329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 25166 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) : 0.6245066 object centre at (A) : 63.72550 59.14500 45.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4092568E-02 -2.0573724E-02 midg,1,midg; midg,igrid,midg 3.9528441E-03 -4.2253081E-02 1,midg,midg; igrid,midg,midg -2.0231590E-02 1.3963753E-02 gauss-seidel spectral radius is 0.9986440 estimated iterations to convergence 215 setup time was (sec) 0.9600000 now iterating at: 11:36:55 rms-change max change #iterations 4.796443 195.3366 at 10iterations 2.244935 67.65721 at 20iterations 1.059510 32.49740 at 30iterations 0.4964697 13.74011 at 40iterations 0.2336774 7.726459 at 50iterations 0.1101036 3.311005 at 60iterations 5.1744785E-02 1.425017 at 70iterations 2.4381477E-02 0.7044258 at 80iterations 1.1444357E-02 0.3710804 at 90iterations 5.3996481E-03 0.1658249 at 100iterations 2.5305916E-03 6.9858551E-02 at 110iterations 1.1975786E-03 3.5369277E-02 at 120iterations finished qdiffx linear iterations at : 11:37:01 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.1975786E-03 3.5369277E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 11:37:02 7.784u 0.194s 0:08.33 95.6% 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 Sat Oct 8 2011 at 11:37:02 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 !!! WARNING: HIR 14 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.810280 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): 35.22300 92.22800 ymin,ymax (A): 33.85500 84.43500 zmin,zma (A): 20.75400 69.76800 x,y,z range (A): 57.00500 50.58000 49.01400 scale (grids/A): 2.810280 object centre (A): 63.72550 59.14500 45.26100 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -5.485964 assigned positive charge : 511.3104 centred at (gu) : 90.97874 89.90630 86.84631 assigned negative charge : -516.7974 centred at (gu) : 90.62637 90.66208 86.84296 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 208218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25168 grid for indexing accessible points = 1.400000 m= 107093 mr = 156991 m= 39225 mr = 89781 m= 9168 mr = 32809 m= 1253 mr = 7110 m= 70 mr = 795 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 9685 time to turn everything in is 1.670000 number of dielectric boundary points 77511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 25632 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) : 1.873520 object centre at (A) : 63.72550 59.14500 45.26100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3191464 -0.2912272 midg,1,midg; midg,igrid,midg -4.0219549E-02 -0.4748278 1,midg,midg; igrid,midg,midg 0.2194549 0.1730035 gauss-seidel spectral radius is 0.9992621 estimated iterations to convergence 291 setup time was (sec) 1.990000 now iterating at: 11:37:04 rms-change max change #iterations 11.19900 309.1812 at 10iterations 6.534280 135.0647 at 20iterations 3.779836 65.46605 at 30iterations 2.189677 35.92577 at 40iterations 1.264294 19.47696 at 50iterations 0.7283915 12.02914 at 60iterations 0.4201699 7.281660 at 70iterations 0.2419216 4.121181 at 80iterations 0.1394523 2.278385 at 90iterations 8.0216855E-02 1.320012 at 100iterations 4.6075314E-02 0.7911370 at 110iterations 2.6582208E-02 0.4479038 at 120iterations 1.5235974E-02 0.2364426 at 130iterations 8.7749232E-03 0.1450601 at 140iterations 5.0527672E-03 8.6006165E-02 at 150iterations 2.9040948E-03 4.7070503E-02 at 160iterations 1.6706713E-03 2.8602600E-02 at 170iterations 9.6080656E-04 1.5401363E-02 at 180iterations finished qdiffx linear iterations at : 11:37:15 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 9.6080656E-04 1.5401363E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 11:37:15 12.861u 0.197s 0:13.42 97.2% 0+0k 0+0io 0pf+0w