Sun Oct 9 16:45:17 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 16:45:17 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 = 2400 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: 0.6609606 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): -55.48900 -6.820000 ymin,ymax (A): -13.67200 34.58100 zmin,zma (A): -3.690000 50.17100 x,y,z range (A): 48.66900 48.25300 53.86100 scale (grids/A): 0.6609606 object centre (A): -31.15450 10.45450 23.24050 number of atom coordinates read : 2400 total number of charged atoms : 2325 net assigned charge : -0.9999937 assigned positive charge : 357.3699 centred at (gu) : 88.84652 91.09017 88.72950 assigned negative charge : -358.3709 centred at (gu) : 88.87585 91.00339 88.86372 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7292 nv = 96 ne = 84 npr = 47218 no. pairs analyzed = 47218 no. exposed pairs = 3135 no. arc points = 22209 no. surface atoms = 1061 nbur = 1339 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 3905 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8244909E-08 -2.1917907E-08 midg,1,midg; midg,igrid,midg -1.5556692E-08 1.6253232E-08 1,midg,midg; igrid,midg,midg 2.9318914E-09 -6.8422179E-09 gauss-seidel spectral radius is 0.9881256 estimated iterations to convergence 75 setup time was (sec) 0.4800000 now iterating at: 16:45:18 rms-change max change #iterations 0.1576091 25.80129 at 10iterations 1.6846405E-02 2.655586 at 20iterations 1.7851510E-03 0.2448730 at 30iterations 2.0078184E-04 2.8030396E-02 at 40iterations 2.7949915E-05 4.5089722E-03 at 50iterations finished qdiffx linear iterations at : 16:45:20 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.7949915E-05 4.5089722E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 16:45:21 3.086u 0.153s 0:03.51 92.0% 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 16:45:21 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 = 2400 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: 1.982882 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): -55.48900 -6.820000 ymin,ymax (A): -13.67200 34.58100 zmin,zma (A): -3.690000 50.17100 x,y,z range (A): 48.66900 48.25300 53.86100 scale (grids/A): 1.982882 object centre (A): -31.15450 10.45450 23.24050 number of atom coordinates read : 2400 total number of charged atoms : 2325 net assigned charge : -0.9999937 assigned positive charge : 357.3699 centred at (gu) : 86.53900 93.26981 86.18803 assigned negative charge : -358.3709 centred at (gu) : 86.62717 93.01032 86.59106 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 28971 mr = 53424 m= 5103 mr = 21126 m= 379 mr = 3284 m= 10 mr = 174 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 34384 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 18398 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) : 0.6609606 object centre at (A) : -31.15450 10.45450 23.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1941270E-02 -6.3854810E-03 midg,1,midg; midg,igrid,midg -1.1134938E-03 -5.9352000E-03 1,midg,midg; igrid,midg,midg 5.6105489E-03 -2.4781844E-02 gauss-seidel spectral radius is 0.9987261 estimated iterations to convergence 222 setup time was (sec) 0.8100000 now iterating at: 16:45:22 rms-change max change #iterations 4.398806 195.6662 at 10iterations 2.113281 71.55521 at 20iterations 1.014365 30.47701 at 30iterations 0.4891932 17.85454 at 40iterations 0.2352213 7.094035 at 50iterations 0.1129418 3.449198 at 60iterations 5.4370049E-02 1.771710 at 70iterations 2.6176425E-02 0.8827295 at 80iterations 1.2579809E-02 0.3819885 at 90iterations 6.0829394E-03 0.1872115 at 100iterations 2.9331422E-03 8.9162827E-02 at 110iterations 1.4078866E-03 4.6551704E-02 at 120iterations finished qdiffx linear iterations at : 16:45:28 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 1.4078866E-03 4.6551704E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.900000 DelPhi exited at 16:45:28 6.898u 0.147s 0:07.35 95.6% 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 Sun Oct 9 2011 at 16:45:28 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 = 2400 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: 2.974323 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): -55.48900 -6.820000 ymin,ymax (A): -13.67200 34.58100 zmin,zma (A): -3.690000 50.17100 x,y,z range (A): 48.66900 48.25300 53.86100 scale (grids/A): 2.974323 object centre (A): -31.15450 10.45450 23.24050 number of atom coordinates read : 2400 total number of charged atoms : 2325 net assigned charge : -0.9999937 assigned positive charge : 357.3699 centred at (gu) : 84.80824 94.90467 84.28191 assigned negative charge : -358.3709 centred at (gu) : 84.94073 94.51534 84.88657 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 180132 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22209 grid for indexing accessible points = 1.400000 m= 91436 mr = 129702 m= 35434 mr = 73952 m= 9542 mr = 28465 m= 1549 mr = 7257 m= 151 mr = 1049 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 77732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 18600 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) : 1.982882 object centre at (A) : -31.15450 10.45450 23.24050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5037869E-02 4.6155695E-02 midg,1,midg; midg,igrid,midg 2.1557592E-02 -0.1100133 1,midg,midg; igrid,midg,midg -1.2679146E-02 -0.3074403 gauss-seidel spectral radius is 0.9992864 estimated iterations to convergence 295 setup time was (sec) 1.640000 now iterating at: 16:45:30 rms-change max change #iterations 10.23390 431.0337 at 10iterations 6.064005 151.8486 at 20iterations 3.568832 82.02914 at 30iterations 2.101245 42.30511 at 40iterations 1.229461 28.73282 at 50iterations 0.7202645 12.82489 at 60iterations 0.4205057 7.780175 at 70iterations 0.2458016 4.389843 at 80iterations 0.1433888 2.588036 at 90iterations 8.3538048E-02 1.606140 at 100iterations 4.8687186E-02 0.8689632 at 110iterations 2.8343052E-02 0.5056267 at 120iterations 1.6519230E-02 0.2827792 at 130iterations 9.6029127E-03 0.1716576 at 140iterations 5.5645728E-03 9.9892616E-02 at 150iterations 3.2441858E-03 5.6301117E-02 at 160iterations 1.8876131E-03 3.7136078E-02 at 170iterations 1.0956540E-03 1.8183470E-02 at 180iterations finished qdiffx linear iterations at : 16:45:40 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 1.0956540E-03 1.8183470E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.28000 DelPhi exited at 16:45:40 11.286u 0.173s 0:11.72 97.6% 0+0k 0+0io 0pf+0w