Sun Oct 9 07:57:59 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 07:57:59 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 = 2128 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: 0.6952311 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): -10.93100 40.27500 ymin,ymax (A): 41.47500 82.67700 zmin,zma (A): 9.932000 59.10800 x,y,z range (A): 51.20600 41.20200 49.17600 scale (grids/A): 0.6952311 object centre (A): 14.67200 62.07600 34.52000 number of atom coordinates read : 2128 total number of charged atoms : 1991 net assigned charge : 8.000017 assigned positive charge : 314.1028 centred at (gu) : 88.75294 89.25829 89.28931 assigned negative charge : -306.1029 centred at (gu) : 88.89333 89.36749 89.33464 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7034 nv = 96 ne = 84 npr = 42883 no. pairs analyzed = 42883 no. exposed pairs = 2732 no. arc points = 19230 no. surface atoms = 926 nbur = 1202 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3860 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.2500000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1856 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7803 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5387376E-08 2.8407724E-08 midg,1,midg; midg,igrid,midg 1.0268622E-07 7.7491773E-09 1,midg,midg; igrid,midg,midg 1.2792431E-07 -1.8969286E-09 gauss-seidel spectral radius is 0.9892311 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 07:57:59 rms-change max change #iterations 0.1875708 32.71179 at 10iterations 2.1952780E-02 2.921341 at 20iterations 2.6035816E-03 0.3621788 at 30iterations 3.0564313E-04 3.9464951E-02 at 40iterations 3.6320878E-05 4.8031807E-03 at 50iterations finished qdiffx linear iterations at : 07:58:02 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 3.6320878E-05 4.8031807E-03 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 07:58:03 3.344u 0.194s 0:04.00 88.2% 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 Sun Oct 9 2011 at 07:58:03 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 = 2128 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.085693 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): -10.93100 40.27500 ymin,ymax (A): 41.47500 82.67700 zmin,zma (A): 9.932000 59.10800 x,y,z range (A): 51.20600 41.20200 49.17600 scale (grids/A): 2.085693 object centre (A): 14.67200 62.07600 34.52000 number of atom coordinates read : 2128 total number of charged atoms : 1991 net assigned charge : 8.000017 assigned positive charge : 314.1028 centred at (gu) : 86.25874 87.77464 87.86804 assigned negative charge : -306.1029 centred at (gu) : 86.67989 88.10253 88.00392 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19230 grid for indexing accessible points = 1.400000 m= 28668 mr = 50247 m= 5710 mr = 21491 m= 519 mr = 3901 m= 12 mr = 249 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.5400000 number of dielectric boundary points 32847 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 15799 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) : 0.6952311 object centre at (A) : 14.67200 62.07600 34.52000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9331425E-02 2.4843644E-02 midg,1,midg; midg,igrid,midg 7.2211154E-02 1.2548625E-03 1,midg,midg; igrid,midg,midg 5.5243570E-02 2.7173496E-04 gauss-seidel spectral radius is 0.9988074 estimated iterations to convergence 229 setup time was (sec) 0.8300000 now iterating at: 07:58:04 rms-change max change #iterations 4.427267 215.2090 at 10iterations 2.166751 74.25496 at 20iterations 1.066101 32.07560 at 30iterations 0.5241234 16.76613 at 40iterations 0.2569204 8.184160 at 50iterations 0.1259374 3.921192 at 60iterations 6.1821003E-02 1.869429 at 70iterations 3.0462796E-02 0.9970245 at 80iterations 1.4950128E-02 0.4439888 at 90iterations 7.3348670E-03 0.2326260 at 100iterations 3.6152736E-03 0.1163216 at 110iterations 1.7795619E-03 5.5004120E-02 at 120iterations finished qdiffx linear iterations at : 07:58:10 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 1.7795619E-03 5.5004120E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 07:58:11 7.622u 0.252s 0:08.16 96.4% 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 Sun Oct 9 2011 at 07:58:11 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 = 2128 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.128540 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): -10.93100 40.27500 ymin,ymax (A): 41.47500 82.67700 zmin,zma (A): 9.932000 59.10800 x,y,z range (A): 51.20600 41.20200 49.17600 scale (grids/A): 3.128540 object centre (A): 14.67200 62.07600 34.52000 number of atom coordinates read : 2128 total number of charged atoms : 1991 net assigned charge : 8.000017 assigned positive charge : 314.1028 centred at (gu) : 84.38812 86.66193 86.80181 assigned negative charge : -306.1029 centred at (gu) : 85.01986 87.15384 87.00576 start vw surface at 0.1400000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 170104 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19230 grid for indexing accessible points = 1.400000 m= 89144 mr = 121576 m= 36732 mr = 73215 m= 10941 mr = 30207 m= 2115 mr = 8567 m= 200 mr = 1552 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 791 time to turn everything in is 1.700000 number of dielectric boundary points 74040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 15920 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) : 2.085693 object centre at (A) : 14.67200 62.07600 34.52000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0607472E-02 0.3728524 midg,1,midg; midg,igrid,midg 0.6809705 -2.2898583E-02 1,midg,midg; igrid,midg,midg 0.2738900 9.4227985E-02 gauss-seidel spectral radius is 0.9992940 estimated iterations to convergence 297 setup time was (sec) 2.010000 now iterating at: 07:58:13 rms-change max change #iterations 9.918401 393.8778 at 10iterations 5.804040 110.3296 at 20iterations 3.389864 65.57442 at 30iterations 1.979162 35.63625 at 40iterations 1.152966 20.55369 at 50iterations 0.6725051 12.31454 at 60iterations 0.3909726 6.539698 at 70iterations 0.2277799 4.059678 at 80iterations 0.1322985 2.389742 at 90iterations 7.7051565E-02 1.313092 at 100iterations 4.4741429E-02 0.7921600 at 110iterations 2.6015472E-02 0.4393177 at 120iterations 1.5118064E-02 0.2658386 at 130iterations 8.7979222E-03 0.1610069 at 140iterations 5.1148250E-03 0.1030388 at 150iterations 2.9750997E-03 4.9650192E-02 at 160iterations 1.7307949E-03 2.9432297E-02 at 170iterations 1.0056017E-03 1.6317368E-02 at 180iterations finished qdiffx linear iterations at : 07:58:24 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 1.0056017E-03 1.6317368E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 07:58:24 12.818u 0.258s 0:13.33 97.9% 0+0k 0+0io 0pf+0w