Sun Oct 9 14:01:52 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 14:01:53 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 0.6754449 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 0.6754449 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500027 assigned positive charge : 366.0292 centred at (gu) : 90.61029 90.65768 90.26872 assigned negative charge : -363.5295 centred at (gu) : 90.79739 90.61370 90.13003 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7380 nv = 96 ne = 84 npr = 47534 no. pairs analyzed = 47534 no. exposed pairs = 2982 no. arc points = 20825 no. surface atoms = 1007 nbur = 1369 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 4074 m= 3 mr = 59 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 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8446 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6999379E-08 4.9746163E-08 midg,1,midg; midg,igrid,midg -1.9065183E-09 2.4842540E-08 1,midg,midg; igrid,midg,midg 5.2784710E-08 -4.8069285E-08 gauss-seidel spectral radius is 0.9886173 estimated iterations to convergence 76 setup time was (sec) 0.4800000 now iterating at: 14:01:53 rms-change max change #iterations 0.1842260 25.51023 at 10iterations 2.0724947E-02 3.149723 at 20iterations 2.8653345E-03 0.4948788 at 30iterations 6.0806458E-04 9.7671509E-02 at 40iterations 1.7623774E-04 2.8976440E-02 at 50iterations finished qdiffx linear iterations at : 14:01:56 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.7623774E-04 2.8976440E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:01:56 3.078u 0.146s 0:03.49 91.9% 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 14:01:56 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 2.026335 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 2.026335 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500027 assigned positive charge : 366.0292 centred at (gu) : 91.83046 91.97246 90.80569 assigned negative charge : -363.5295 centred at (gu) : 92.39165 91.84084 90.38989 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 78682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20825 grid for indexing accessible points = 1.400000 m= 29470 mr = 54647 m= 4981 mr = 21899 m= 350 mr = 3165 m= 9 mr = 150 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 33628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17679 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) : 0.6754449 object centre at (A) : 12.97100 -5.813001 -12.62050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7691370E-03 6.7199200E-02 midg,1,midg; midg,igrid,midg 4.3296933E-02 5.0303001E-02 1,midg,midg; igrid,midg,midg 4.2865644E-03 -3.3449896E-02 gauss-seidel spectral radius is 0.9987703 estimated iterations to convergence 226 setup time was (sec) 0.8100000 now iterating at: 14:01:57 rms-change max change #iterations 4.680768 203.5988 at 10iterations 2.271482 73.63976 at 20iterations 1.111264 34.31630 at 30iterations 0.5393947 16.23694 at 40iterations 0.2621369 7.435532 at 50iterations 0.1277857 4.023377 at 60iterations 6.2634759E-02 1.945966 at 70iterations 3.0625273E-02 0.9352665 at 80iterations 1.5041252E-02 0.4519377 at 90iterations 7.4540800E-03 0.2269783 at 100iterations 3.7941788E-03 0.1175842 at 110iterations 1.9791280E-03 6.5536499E-02 at 120iterations finished qdiffx linear iterations at : 14:02:03 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 1.9791280E-03 6.5536499E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 14:02:04 6.990u 0.165s 0:07.49 95.4% 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 14:02:04 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 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: 3.039502 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): -11.71600 37.65800 ymin,ymax (A): -32.16600 20.54000 zmin,zma (A): -36.71700 11.47600 x,y,z range (A): 49.37400 52.70600 48.19300 scale (grids/A): 3.039502 object centre (A): 12.97100 -5.813001 -12.62050 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 2.500027 assigned positive charge : 366.0292 centred at (gu) : 92.74562 92.95858 91.20841 assigned negative charge : -363.5295 centred at (gu) : 93.58742 92.76133 90.58466 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 181895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20825 grid for indexing accessible points = 1.400000 m= 94397 mr = 132453 m= 35170 mr = 77504 m= 9040 mr = 28349 m= 1584 mr = 6881 m= 139 mr = 1134 m= 9 mr = 79 m= 0 mr = 4 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 75830 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 17868 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) : 2.026335 object centre at (A) : 12.97100 -5.813001 -12.62050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1078685 0.8406666 midg,1,midg; midg,igrid,midg 1.195009 0.9868316 1,midg,midg; igrid,midg,midg 2.2167725E-02 -0.3752852 gauss-seidel spectral radius is 0.9992863 estimated iterations to convergence 295 setup time was (sec) 1.650000 now iterating at: 14:02:05 rms-change max change #iterations 10.63504 412.0934 at 10iterations 6.255687 132.9525 at 20iterations 3.683818 69.50748 at 30iterations 2.159502 41.61871 at 40iterations 1.263409 25.08031 at 50iterations 0.7387337 14.80669 at 60iterations 0.4314617 7.545415 at 70iterations 0.2518570 4.492236 at 80iterations 0.1468835 2.503328 at 90iterations 8.5691139E-02 1.718479 at 100iterations 5.0083708E-02 0.8568544 at 110iterations 2.9345302E-02 0.5283318 at 120iterations 1.7278962E-02 0.3128967 at 130iterations 1.0329280E-02 0.2029877 at 140iterations 6.3111461E-03 0.1273003 at 150iterations 3.9937031E-03 8.7270737E-02 at 160iterations 2.6629406E-03 6.0333252E-02 at 170iterations 1.8890110E-03 4.4956207E-02 at 180iterations finished qdiffx linear iterations at : 14:02:15 total time elapsed so far: 11.11000 # loops : 180 mean,max change (kT/e) : 1.8890110E-03 4.4956207E-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) 11.29000 DelPhi exited at 14:02:15 11.292u 0.176s 0:11.73 97.6% 0+0k 0+0io 0pf+0w