Mon Oct 10 14:00:51 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 Mon Oct 10 2011 at 14:00:51 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 0.6552550 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): -0.2530000 54.07700 ymin,ymax (A): 8.046000 49.82500 zmin,zma (A): -12.43500 39.45300 x,y,z range (A): 54.33000 41.77900 51.88800 scale (grids/A): 0.6552550 object centre (A): 26.91200 28.93550 13.50900 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 14.00002 assigned positive charge : 343.6123 centred at (gu) : 89.66090 90.87803 91.54100 assigned negative charge : -329.6130 centred at (gu) : 89.65171 90.88078 91.51880 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6755 nv = 96 ne = 84 npr = 47265 no. pairs analyzed = 47265 no. exposed pairs = 3015 no. arc points = 21472 no. surface atoms = 1007 nbur = 1332 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 3557 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.3400000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2068 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0487589E-08 4.7186308E-08 midg,1,midg; midg,igrid,midg 2.6430953E-08 3.6705384E-08 1,midg,midg; igrid,midg,midg 3.1869568E-08 3.0336405E-08 gauss-seidel spectral radius is 0.9879114 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 14:00:52 rms-change max change #iterations 0.1469000 26.43279 at 10iterations 1.5634684E-02 2.121570 at 20iterations 1.6719998E-03 0.2533884 at 30iterations 2.2664956E-04 3.5510063E-02 at 40iterations 5.5539404E-05 1.1659145E-02 at 50iterations finished qdiffx linear iterations at : 14:00:55 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 5.5539404E-05 1.1659145E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 14:00:56 4.194u 0.231s 0:04.82 91.7% 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 Mon Oct 10 2011 at 14:00:56 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 1.965765 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): -0.2530000 54.07700 ymin,ymax (A): 8.046000 49.82500 zmin,zma (A): -12.43500 39.45300 x,y,z range (A): 54.33000 41.77900 51.88800 scale (grids/A): 1.965765 object centre (A): 26.91200 28.93550 13.50900 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 14.00002 assigned positive charge : 343.6123 centred at (gu) : 88.98250 92.63379 94.62261 assigned negative charge : -329.6130 centred at (gu) : 88.95508 92.64227 94.55640 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21472 grid for indexing accessible points = 1.400000 m= 25999 mr = 48595 m= 4560 mr = 18789 m= 314 mr = 2882 m= 4 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1952 time to turn everything in is 0.6400000 number of dielectric boundary points 32734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17400 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) : 0.6552550 object centre at (A) : 26.91200 28.93550 13.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9427807E-02 3.4019232E-02 midg,1,midg; midg,igrid,midg 1.3494263E-02 3.4347638E-02 1,midg,midg; igrid,midg,midg 5.3212728E-02 5.1937480E-02 gauss-seidel spectral radius is 0.9986953 estimated iterations to convergence 219 setup time was (sec) 0.9700000 now iterating at: 14:00:57 rms-change max change #iterations 4.108158 177.1169 at 10iterations 1.955484 73.31151 at 20iterations 0.9314129 35.31924 at 30iterations 0.4423392 17.08195 at 40iterations 0.2112259 6.770940 at 50iterations 0.1004679 3.152269 at 60iterations 4.7584787E-02 1.618341 at 70iterations 2.2694854E-02 0.7053673 at 80iterations 1.0818063E-02 0.3606415 at 90iterations 5.1816013E-03 0.1677952 at 100iterations 2.4859218E-03 7.8564644E-02 at 110iterations 1.1985970E-03 3.6101580E-02 at 120iterations finished qdiffx linear iterations at : 14:01:06 total time elapsed so far: 9.560000 # loops : 120 mean,max change (kT/e) : 1.1985970E-03 3.6101580E-02 energy calculations done at 9.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.780000 DelPhi exited at 14:01:07 9.783u 0.279s 0:10.76 93.4% 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 Mon Oct 10 2011 at 14:01:07 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 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: 2.948647 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): -0.2530000 54.07700 ymin,ymax (A): 8.046000 49.82500 zmin,zma (A): -12.43500 39.45300 x,y,z range (A): 54.33000 41.77900 51.88800 scale (grids/A): 2.948647 object centre (A): 26.91200 28.93550 13.50900 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 14.00002 assigned positive charge : 343.6123 centred at (gu) : 88.47374 93.95065 96.93382 assigned negative charge : -329.6130 centred at (gu) : 88.43255 93.96356 96.83460 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 166922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21472 grid for indexing accessible points = 1.400000 m= 83079 mr = 118377 m= 31173 mr = 66851 m= 8346 mr = 24783 m= 1395 mr = 6288 m= 82 mr = 952 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 6918 time to turn everything in is 1.630000 number of dielectric boundary points 73705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 17631 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) : 1.965765 object centre at (A) : 26.91200 28.93550 13.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6716173 0.3599559 midg,1,midg; midg,igrid,midg 8.9150481E-02 0.3194316 1,midg,midg; igrid,midg,midg 0.5487376 0.4863546 gauss-seidel spectral radius is 0.9992781 estimated iterations to convergence 294 setup time was (sec) 2.000000 now iterating at: 14:01:09 rms-change max change #iterations 9.717327 416.9671 at 10iterations 5.750542 139.2412 at 20iterations 3.378785 72.76437 at 30iterations 1.986601 42.09839 at 40iterations 1.159582 23.32105 at 50iterations 0.6765066 13.21823 at 60iterations 0.3947583 7.536460 at 70iterations 0.2293312 4.579765 at 80iterations 0.1336446 2.657284 at 90iterations 7.7602141E-02 1.425757 at 100iterations 4.5057595E-02 0.8043289 at 110iterations 2.6176168E-02 0.5139198 at 120iterations 1.5173152E-02 0.2780471 at 130iterations 8.8204267E-03 0.1697369 at 140iterations 5.1321480E-03 9.7854614E-02 at 150iterations 2.9921676E-03 5.4225922E-02 at 160iterations 1.7585952E-03 3.2726288E-02 at 170iterations 1.0445641E-03 2.3656368E-02 at 180iterations finished qdiffx linear iterations at : 14:01:23 total time elapsed so far: 16.21000 # loops : 180 mean,max change (kT/e) : 1.0445641E-03 2.3656368E-02 energy calculations done at 16.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.43000 DelPhi exited at 14:01:24 16.431u 0.321s 0:17.05 98.2% 0+0k 0+0io 0pf+0w