Sat Oct 15 12:55:03 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 15 2011 at 12:55:03 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 218 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5935312 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): -49.87800 10.10200 ymin,ymax (A): -25.10700 26.70700 zmin,zma (A): -29.68100 26.46300 x,y,z range (A): 59.98000 51.81400 56.14400 scale (grids/A): 0.5935312 object centre (A): -19.88800 0.8000002 -1.609000 number of atom coordinates read : 2869 total number of charged atoms : 2799 net assigned charge : 4.514016 assigned positive charge : 431.2599 centred at (gu) : 89.74356 90.63602 91.60636 assigned negative charge : -426.7478 centred at (gu) : 89.75506 90.56527 91.52769 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7093 nv = 96 ne = 84 npr = 54190 no. pairs analyzed = 54190 no. exposed pairs = 4058 no. arc points = 28963 no. surface atoms = 1345 nbur = 1524 mkacc time = 0.1200000 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= 386 mr = 3539 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2870 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8800 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3736461E-10 5.8613940E-09 midg,1,midg; midg,igrid,midg -7.1048695E-10 4.3839781E-09 1,midg,midg; igrid,midg,midg 1.9814392E-09 1.0587876E-09 gauss-seidel spectral radius is 0.9853527 estimated iterations to convergence 68 setup time was (sec) 0.5200000 now iterating at: 12:55:04 rms-change max change #iterations 0.1073873 20.52534 at 10iterations 9.1896886E-03 1.431177 at 20iterations 9.5673028E-04 0.1296730 at 30iterations 1.7526626E-04 2.7468204E-02 at 40iterations 4.5227029E-05 7.4081421E-03 at 50iterations finished qdiffx linear iterations at : 12:55:06 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 4.5227029E-05 7.4081421E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 12:55:06 3.141u 0.147s 0:03.56 92.1% 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 15 2011 at 12:55:06 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 218 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.780594 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): -49.87800 10.10200 ymin,ymax (A): -25.10700 26.70700 zmin,zma (A): -29.68100 26.46300 x,y,z range (A): 59.98000 51.81400 56.14400 scale (grids/A): 1.780594 object centre (A): -19.88800 0.8000002 -1.609000 number of atom coordinates read : 2869 total number of charged atoms : 2799 net assigned charge : 4.514016 assigned positive charge : 431.2599 centred at (gu) : 89.22978 91.90702 94.81818 assigned negative charge : -426.7478 centred at (gu) : 89.26528 91.69545 94.58295 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28963 grid for indexing accessible points = 1.400000 m= 27065 mr = 50859 m= 4105 mr = 18677 m= 205 mr = 2312 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 208 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21856 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) : 0.5935312 object centre at (A) : -19.88800 0.8000002 -1.609000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0647429E-03 1.5142950E-02 midg,1,midg; midg,igrid,midg 1.2012344E-02 3.1198671E-02 1,midg,midg; igrid,midg,midg 1.5552443E-02 -2.0069914E-02 gauss-seidel spectral radius is 0.9985003 estimated iterations to convergence 205 setup time was (sec) 0.8100000 now iterating at: 12:55:07 rms-change max change #iterations 3.917286 171.5910 at 10iterations 1.764450 63.49884 at 20iterations 0.7950011 27.54395 at 30iterations 0.3575810 12.59156 at 40iterations 0.1615044 5.297629 at 50iterations 7.2845459E-02 2.397665 at 60iterations 3.2776698E-02 1.105293 at 70iterations 1.4848444E-02 0.5068207 at 80iterations 6.7552123E-03 0.2248402 at 90iterations 3.0502167E-03 0.1038342 at 100iterations 1.3930986E-03 4.6567440E-02 at 110iterations 6.4274273E-04 2.0945549E-02 at 120iterations finished qdiffx linear iterations at : 12:55:14 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 6.4274273E-04 2.0945549E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 12:55:14 7.165u 0.166s 0:07.90 92.6% 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 15 2011 at 12:55:14 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2869 !!! WARNING: HIR 218 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.670890 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): -49.87800 10.10200 ymin,ymax (A): -25.10700 26.70700 zmin,zma (A): -29.68100 26.46300 x,y,z range (A): 59.98000 51.81400 56.14400 scale (grids/A): 2.670890 object centre (A): -19.88800 0.8000002 -1.609000 number of atom coordinates read : 2869 total number of charged atoms : 2799 net assigned charge : 4.514016 assigned positive charge : 431.2599 centred at (gu) : 88.84450 92.86054 97.22697 assigned negative charge : -426.7478 centred at (gu) : 88.89794 92.54310 96.87447 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 178038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28963 grid for indexing accessible points = 1.400000 m= 87105 mr = 124619 m= 31071 mr = 68268 m= 7211 mr = 23876 m= 881 mr = 4915 m= 47 mr = 515 m= 0 mr = 4 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 82156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 22385 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) : 1.780594 object centre at (A) : -19.88800 0.8000002 -1.609000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6328588E-02 0.1710115 midg,1,midg; midg,igrid,midg 0.2201723 0.4200987 1,midg,midg; igrid,midg,midg 0.2627155 -0.3209923 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 1.620000 now iterating at: 12:55:16 rms-change max change #iterations 9.787123 339.1248 at 10iterations 5.808956 138.8757 at 20iterations 3.396900 95.83613 at 30iterations 1.981287 41.92649 at 40iterations 1.147076 23.56611 at 50iterations 0.6634953 13.13088 at 60iterations 0.3821316 8.540009 at 70iterations 0.2196788 4.286129 at 80iterations 0.1264510 2.558075 at 90iterations 7.2353087E-02 1.417124 at 100iterations 4.1516319E-02 0.8196883 at 110iterations 2.3771381E-02 0.4420776 at 120iterations 1.3625063E-02 0.2630224 at 130iterations 7.7853473E-03 0.1518917 at 140iterations 4.4675590E-03 7.9059601E-02 at 150iterations 2.5551184E-03 5.0300598E-02 at 160iterations 1.4600172E-03 2.6887894E-02 at 170iterations 8.3952979E-04 1.6778946E-02 at 180iterations finished qdiffx linear iterations at : 12:55:26 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 8.3952979E-04 1.6778946E-02 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 12:55:27 11.698u 0.187s 0:12.36 96.0% 0+0k 0+0io 0pf+0w