Mon Oct 10 17:05:06 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+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 Mon Oct 10 2011 at 17:05:06 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 = 2603 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6087239 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): 16.12400 71.54601 ymin,ymax (A): -37.35600 8.314000 zmin,zma (A): -31.09400 27.38900 x,y,z range (A): 55.42200 45.67000 58.48300 scale (grids/A): 0.6087239 object centre (A): 43.83500 -14.52100 -1.852500 number of atom coordinates read : 2603 total number of charged atoms : 2465 net assigned charge : 3.000014 assigned positive charge : 387.8749 centred at (gu) : 91.32924 89.34464 89.03139 assigned negative charge : -384.8755 centred at (gu) : 91.31493 89.45370 89.10964 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6550 nv = 96 ne = 84 npr = 52037 no. pairs analyzed = 52037 no. exposed pairs = 3439 no. arc points = 24048 no. surface atoms = 1158 nbur = 1445 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 298 mr = 3437 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.1900000 number of dielectric boundary points 3395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2434 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5520198E-09 -1.6755406E-09 midg,1,midg; midg,igrid,midg 7.7537701E-09 -3.0812362E-09 1,midg,midg; igrid,midg,midg 7.1258011E-10 3.0664886E-09 gauss-seidel spectral radius is 0.9860357 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 17:05:06 rms-change max change #iterations 0.1099449 15.07848 at 10iterations 9.7970087E-03 1.349373 at 20iterations 8.5867028E-04 0.1324863 at 30iterations 8.5922948E-05 1.4409065E-02 at 40iterations 1.1695254E-05 2.3155212E-03 at 50iterations finished qdiffx linear iterations at : 17:05:09 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.1695254E-05 2.3155212E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 17:05:10 3.371u 0.181s 0:04.78 74.2% 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 Mon Oct 10 2011 at 17:05:10 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 = 2603 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.826172 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): 16.12400 71.54601 ymin,ymax (A): -37.35600 8.314000 zmin,zma (A): -31.09400 27.38900 x,y,z range (A): 55.42200 45.67000 58.48300 scale (grids/A): 1.826172 object centre (A): 43.83500 -14.52100 -1.852500 number of atom coordinates read : 2603 total number of charged atoms : 2465 net assigned charge : 3.000014 assigned positive charge : 387.8749 centred at (gu) : 93.98716 88.03342 87.09371 assigned negative charge : -384.8755 centred at (gu) : 93.94460 88.36090 87.32832 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70854 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 23391 mr = 47841 m= 2995 mr = 16488 m= 143 mr = 1684 m= 4 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 135 time to turn everything in is 0.3500000 number of dielectric boundary points 31336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19313 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) : 0.6087239 object centre at (A) : 43.83500 -14.52100 -1.852500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1243290E-03 -1.8850140E-02 midg,1,midg; midg,igrid,midg 1.6768264E-02 -4.3228888E-03 1,midg,midg; igrid,midg,midg 2.3001187E-02 2.0560591E-02 gauss-seidel spectral radius is 0.9985238 estimated iterations to convergence 206 setup time was (sec) 0.5900000 now iterating at: 17:05:11 rms-change max change #iterations 3.858040 201.7938 at 10iterations 1.744917 61.53352 at 20iterations 0.7924101 27.90941 at 30iterations 0.3590535 11.38309 at 40iterations 0.1629889 6.360762 at 50iterations 7.4134327E-02 2.324783 at 60iterations 3.3649966E-02 1.104168 at 70iterations 1.5299045E-02 0.5587435 at 80iterations 6.9609503E-03 0.2256241 at 90iterations 3.1496808E-03 0.1092911 at 100iterations 1.4326625E-03 4.6070099E-02 at 110iterations 6.4903492E-04 2.1542549E-02 at 120iterations finished qdiffx linear iterations at : 17:05:19 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 6.4903492E-04 2.1542549E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.360000 DelPhi exited at 17:05:19 8.358u 0.248s 0:08.95 95.9% 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 Mon Oct 10 2011 at 17:05:20 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 = 2603 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.739258 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): 16.12400 71.54601 ymin,ymax (A): -37.35600 8.314000 zmin,zma (A): -31.09400 27.38900 x,y,z range (A): 55.42200 45.67000 58.48300 scale (grids/A): 2.739258 object centre (A): 43.83500 -14.52100 -1.852500 number of atom coordinates read : 2603 total number of charged atoms : 2465 net assigned charge : 3.000014 assigned positive charge : 387.8749 centred at (gu) : 95.98051 87.05003 85.64043 assigned negative charge : -384.8755 centred at (gu) : 95.91688 87.54121 85.99245 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 164305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24048 grid for indexing accessible points = 1.400000 m= 78205 mr = 116983 m= 24889 mr = 62323 m= 4892 mr = 19128 m= 521 mr = 3444 m= 27 mr = 266 m= 0 mr = 7 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 0.8800000 number of dielectric boundary points 70688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 19715 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) : 1.826172 object centre at (A) : 43.83500 -14.52100 -1.852500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7836027E-02 9.4170853E-02 midg,1,midg; midg,igrid,midg 0.2222736 -2.0455461E-02 1,midg,midg; igrid,midg,midg 0.2071944 0.2326040 gauss-seidel spectral radius is 0.9992411 estimated iterations to convergence 287 setup time was (sec) 1.110000 now iterating at: 17:05:21 rms-change max change #iterations 9.312444 371.0206 at 10iterations 5.364120 122.3504 at 20iterations 3.075398 75.04790 at 30iterations 1.762469 37.72687 at 40iterations 1.010693 18.33857 at 50iterations 0.5761051 10.70758 at 60iterations 0.3298793 6.352240 at 70iterations 0.1877518 3.416779 at 80iterations 0.1067221 2.033572 at 90iterations 6.0909066E-02 1.116919 at 100iterations 3.4673538E-02 0.6594849 at 110iterations 1.9740256E-02 0.3590345 at 120iterations 1.1264153E-02 0.2025719 at 130iterations 6.4314133E-03 0.1203461 at 140iterations 3.6488117E-03 6.7863464E-02 at 150iterations 2.0800917E-03 3.8204193E-02 at 160iterations 1.1867338E-03 2.2764206E-02 at 170iterations 6.7520194E-04 1.2004882E-02 at 180iterations finished qdiffx linear iterations at : 17:05:32 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 6.7520194E-04 1.2004882E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 17:05:33 12.565u 0.247s 0:13.15 97.3% 0+0k 0+0io 0pf+0w