Sun Oct 9 19:39:42 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 Sun Oct 9 2011 at 19:39:42 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3164 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5719978 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): -11.16800 51.07000 ymin,ymax (A): -11.99400 41.27500 zmin,zma (A): 19.76300 76.23100 x,y,z range (A): 62.23800 53.26900 56.46800 scale (grids/A): 0.5719978 object centre (A): 19.95100 14.64050 47.99700 number of atom coordinates read : 3164 total number of charged atoms : 3010 net assigned charge : 3.240031 assigned positive charge : 486.8099 centred at (gu) : 90.55511 89.46798 87.65635 assigned negative charge : -483.5711 centred at (gu) : 90.48515 89.55765 87.65320 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6986 nv = 96 ne = 84 npr = 61143 no. pairs analyzed = 61143 no. exposed pairs = 4288 no. arc points = 30266 no. surface atoms = 1436 nbur = 1728 mkacc time = 0.2100000 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 = 1.484000 m= 347 mr = 3515 m= 4 mr = 22 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 0.4500000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2959 ## 330 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 8726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8665785E-10 3.3594397E-10 midg,1,midg; midg,igrid,midg 2.4157114E-09 -9.9310216E-10 1,midg,midg; igrid,midg,midg -6.6794409E-10 2.0271855E-09 gauss-seidel spectral radius is 0.9842498 estimated iterations to convergence 65 setup time was (sec) 0.8000000 now iterating at: 19:39:43 rms-change max change #iterations 9.3909316E-02 15.45670 at 10iterations 7.2215921E-03 1.039587 at 20iterations 5.5302249E-04 9.8503113E-02 at 30iterations 6.2215651E-05 9.0179443E-03 at 40iterations 2.3503611E-05 3.3183098E-03 at 50iterations finished qdiffx linear iterations at : 19:39:47 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 2.3503611E-05 3.3183098E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 19:39:48 4.697u 0.401s 0:05.37 94.7% 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 19:39:48 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3164 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.715994 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): -11.16800 51.07000 ymin,ymax (A): -11.99400 41.27500 zmin,zma (A): 19.76300 76.23100 x,y,z range (A): 62.23800 53.26900 56.46800 scale (grids/A): 1.715994 object centre (A): 19.95100 14.64050 47.99700 number of atom coordinates read : 3164 total number of charged atoms : 3010 net assigned charge : 3.240031 assigned positive charge : 486.8099 centred at (gu) : 91.66489 88.40308 82.96838 assigned negative charge : -483.5711 centred at (gu) : 91.45511 88.67264 82.95928 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30266 grid for indexing accessible points = 1.400000 m= 25520 mr = 51135 m= 3206 mr = 17255 m= 107 mr = 1505 m= 0 mr = 14 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 35325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 23303 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) : 0.5719978 object centre at (A) : 19.95100 14.64050 47.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5193120E-02 5.5811126E-03 midg,1,midg; midg,igrid,midg 1.9373316E-02 -1.0026183E-02 1,midg,midg; igrid,midg,midg -6.1460887E-03 4.9610864E-03 gauss-seidel spectral radius is 0.9983891 estimated iterations to convergence 198 setup time was (sec) 1.120000 now iterating at: 19:39:49 rms-change max change #iterations 3.901124 176.5121 at 10iterations 1.712488 61.31950 at 20iterations 0.7553775 27.54358 at 30iterations 0.3321047 11.79429 at 40iterations 0.1461326 5.308620 at 50iterations 6.4507633E-02 2.231124 at 60iterations 2.8362783E-02 1.019712 at 70iterations 1.2503128E-02 0.5064554 at 80iterations 5.5189268E-03 0.1834726 at 90iterations 2.4311903E-03 8.0806732E-02 at 100iterations 1.0837128E-03 3.9063454E-02 at 110iterations 4.9803255E-04 1.8464088E-02 at 120iterations finished qdiffx linear iterations at : 19:39:59 total time elapsed so far: 10.60000 # loops : 120 mean,max change (kT/e) : 4.9803255E-04 1.8464088E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.82000 DelPhi exited at 19:39:59 10.820u 0.445s 0:11.59 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 19:39:59 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3164 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.573990 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): -11.16800 51.07000 ymin,ymax (A): -11.99400 41.27500 zmin,zma (A): 19.76300 76.23100 x,y,z range (A): 62.23800 53.26900 56.46800 scale (grids/A): 2.573990 object centre (A): 19.95100 14.64050 47.99700 number of atom coordinates read : 3164 total number of charged atoms : 3010 net assigned charge : 3.240031 assigned positive charge : 486.8099 centred at (gu) : 92.49714 87.60451 79.45230 assigned negative charge : -483.5711 centred at (gu) : 92.18261 88.00885 79.43880 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 177078 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30266 grid for indexing accessible points = 1.400000 m= 85040 mr = 125279 m= 27255 mr = 66280 m= 5132 mr = 20146 m= 505 mr = 3212 m= 16 mr = 279 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.000000 number of dielectric boundary points 79827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 24043 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) : 1.715994 object centre at (A) : 19.95100 14.64050 47.99700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2952696 7.1190834E-02 midg,1,midg; midg,igrid,midg 0.2759045 -0.2032918 1,midg,midg; igrid,midg,midg 0.1260217 0.1088664 gauss-seidel spectral radius is 0.9992116 estimated iterations to convergence 281 setup time was (sec) 2.370000 now iterating at: 19:40:02 rms-change max change #iterations 10.00792 286.2234 at 10iterations 5.889823 149.4487 at 20iterations 3.415375 79.80302 at 30iterations 1.975440 45.96019 at 40iterations 1.134043 26.51604 at 50iterations 0.6478603 14.01136 at 60iterations 0.3700978 7.912834 at 70iterations 0.2112740 4.411850 at 80iterations 0.1197194 2.331837 at 90iterations 6.8157725E-02 1.421459 at 100iterations 3.8766325E-02 0.7768421 at 110iterations 2.1993278E-02 0.5522795 at 120iterations 1.2517956E-02 0.2360966 at 130iterations 7.1399971E-03 0.1432695 at 140iterations 4.1183736E-03 8.2971573E-02 at 150iterations 2.4204841E-03 4.8860550E-02 at 160iterations 1.4913749E-03 3.2129765E-02 at 170iterations 9.8586781E-04 2.1554947E-02 at 180iterations finished qdiffx linear iterations at : 19:40:18 total time elapsed so far: 17.98000 # loops : 180 mean,max change (kT/e) : 9.8586781E-04 2.1554947E-02 energy calculations done at 17.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.19000 DelPhi exited at 19:40:18 18.194u 0.469s 0:18.94 98.4% 0+0k 0+0io 0pf+0w