Sun Oct 9 01:47:39 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 Sun Oct 9 2011 at 01:47:39 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 = 2449 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: 0.5986715 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): -26.69800 27.20200 ymin,ymax (A): 8.252000 50.18300 zmin,zma (A): -11.66100 47.80400 x,y,z range (A): 53.90000 41.93100 59.46500 scale (grids/A): 0.5986715 object centre (A): 0.2519999 29.21750 18.07150 number of atom coordinates read : 2449 total number of charged atoms : 2313 net assigned charge : 10.50003 assigned positive charge : 355.3111 centred at (gu) : 90.22533 91.04078 89.77203 assigned negative charge : -344.8120 centred at (gu) : 90.23035 90.96475 89.80495 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5951 nv = 96 ne = 84 npr = 48566 no. pairs analyzed = 48566 no. exposed pairs = 3218 no. arc points = 23061 no. surface atoms = 1085 nbur = 1364 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 273 mr = 3052 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2319 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5700964E-09 3.0913085E-09 midg,1,midg; midg,igrid,midg 1.5286340E-09 8.3689589E-09 1,midg,midg; igrid,midg,midg 4.2165982E-09 4.3277333E-09 gauss-seidel spectral radius is 0.9855555 estimated iterations to convergence 68 setup time was (sec) 0.3900000 now iterating at: 01:47:39 rms-change max change #iterations 9.9624969E-02 17.22382 at 10iterations 8.4058754E-03 1.345901 at 20iterations 7.2618405E-04 0.1090235 at 30iterations 6.7696725E-05 1.1192322E-02 at 40iterations 7.8908752E-06 1.0299683E-03 at 50iterations finished qdiffx linear iterations at : 01:47:42 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 7.8908752E-06 1.0299683E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 01:47:43 3.565u 0.193s 0:04.18 89.7% 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 Sun Oct 9 2011 at 01:47:43 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 = 2449 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: 1.796014 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): -26.69800 27.20200 ymin,ymax (A): 8.252000 50.18300 zmin,zma (A): -11.66100 47.80400 x,y,z range (A): 53.90000 41.93100 59.46500 scale (grids/A): 1.796014 object centre (A): 0.2519999 29.21750 18.07150 number of atom coordinates read : 2449 total number of charged atoms : 2313 net assigned charge : 10.50003 assigned positive charge : 355.3111 centred at (gu) : 90.67559 93.12205 89.31544 assigned negative charge : -344.8120 centred at (gu) : 90.69098 92.89416 89.41470 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23061 grid for indexing accessible points = 1.400000 m= 20953 mr = 42862 m= 2764 mr = 14609 m= 137 mr = 1527 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 165 time to turn everything in is 0.3300000 number of dielectric boundary points 29320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 18046 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) : 0.5986715 object centre at (A) : 0.2519999 29.21750 18.07150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9653607E-02 1.4583018E-02 midg,1,midg; midg,igrid,midg -4.2756912E-03 1.8864438E-02 1,midg,midg; igrid,midg,midg 2.9253969E-02 3.1458717E-02 gauss-seidel spectral radius is 0.9984639 estimated iterations to convergence 202 setup time was (sec) 0.5900000 now iterating at: 01:47:44 rms-change max change #iterations 3.543509 174.4303 at 10iterations 1.572430 61.73295 at 20iterations 0.7010370 25.45873 at 30iterations 0.3132764 11.06519 at 40iterations 0.1396789 5.356110 at 50iterations 6.2552616E-02 2.223667 at 60iterations 2.7891560E-02 1.040921 at 70iterations 1.2448270E-02 0.4549723 at 80iterations 5.5711758E-03 0.1893473 at 90iterations 2.4982688E-03 8.4095240E-02 at 100iterations 1.1151424E-03 4.2691708E-02 at 110iterations 4.9939053E-04 2.0099640E-02 at 120iterations finished qdiffx linear iterations at : 01:47:52 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 4.9939053E-04 2.0099640E-02 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.660000 DelPhi exited at 01:47:52 8.660u 0.252s 0:09.17 97.1% 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 Sun Oct 9 2011 at 01:47:52 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 = 2449 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: 2.694022 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): -26.69800 27.20200 ymin,ymax (A): 8.252000 50.18300 zmin,zma (A): -11.66100 47.80400 x,y,z range (A): 53.90000 41.93100 59.46500 scale (grids/A): 2.694022 object centre (A): 0.2519999 29.21750 18.07150 number of atom coordinates read : 2449 total number of charged atoms : 2313 net assigned charge : 10.50003 assigned positive charge : 355.3111 centred at (gu) : 91.01334 94.68298 88.97305 assigned negative charge : -344.8120 centred at (gu) : 91.03645 94.34116 89.12213 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 149278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23061 grid for indexing accessible points = 1.400000 m= 70413 mr = 104836 m= 22715 mr = 55745 m= 4702 mr = 17374 m= 529 mr = 3297 m= 23 mr = 284 m= 0 mr = 10 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 634 time to turn everything in is 0.8700000 number of dielectric boundary points 66114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 18495 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) : 1.796014 object centre at (A) : 0.2519999 29.21750 18.07150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6092083 0.2635525 midg,1,midg; midg,igrid,midg -6.7602940E-02 0.2498875 1,midg,midg; igrid,midg,midg 0.3485958 0.3340752 gauss-seidel spectral radius is 0.9992162 estimated iterations to convergence 282 setup time was (sec) 1.180000 now iterating at: 01:47:54 rms-change max change #iterations 8.754404 417.8479 at 10iterations 5.110642 154.3323 at 20iterations 2.943497 88.43301 at 30iterations 1.691261 37.87660 at 40iterations 0.9704757 22.06522 at 50iterations 0.5534717 11.86797 at 60iterations 0.3142425 6.232196 at 70iterations 0.1789239 3.514162 at 80iterations 0.1015240 2.223130 at 90iterations 5.7571329E-02 1.177626 at 100iterations 3.2598443E-02 0.6752243 at 110iterations 1.8511111E-02 0.3745294 at 120iterations 1.0468908E-02 0.2599783 at 130iterations 5.9236968E-03 0.1295815 at 140iterations 3.3487303E-03 6.6399097E-02 at 150iterations 1.8963581E-03 3.6909103E-02 at 160iterations 1.0714268E-03 2.2876740E-02 at 170iterations 6.0648192E-04 1.1213303E-02 at 180iterations finished qdiffx linear iterations at : 01:48:08 total time elapsed so far: 15.15000 # loops : 180 mean,max change (kT/e) : 6.0648192E-04 1.1213303E-02 energy calculations done at 15.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.28000 DelPhi exited at 01:48:08 15.280u 0.304s 0:15.85 98.2% 0+0k 0+0io 0pf+0w