Sat Oct 8 13:53:00 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 Sat Oct 8 2011 at 13:53:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2970 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6341402 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): -11.50700 43.19900 ymin,ymax (A): 11.15700 55.00500 zmin,zma (A): 37.49100 93.63000 x,y,z range (A): 54.70600 43.84800 56.13900 scale (grids/A): 0.6341402 object centre (A): 15.84600 33.08100 65.56050 number of atom coordinates read : 2970 total number of charged atoms : 2823 net assigned charge : -1.499993 assigned positive charge : 445.5066 centred at (gu) : 89.09677 89.47055 91.30522 assigned negative charge : -447.0074 centred at (gu) : 89.08004 89.38573 91.22498 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7986 nv = 96 ne = 84 npr = 62029 no. pairs analyzed = 62029 no. exposed pairs = 3478 no. arc points = 23271 no. surface atoms = 1181 nbur = 1789 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4708 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9709 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.3839513E-09 9.6369677E-09 midg,1,midg; midg,igrid,midg -1.3085347E-08 6.8440213E-09 1,midg,midg; igrid,midg,midg -4.6158237E-09 -1.3119440E-12 gauss-seidel spectral radius is 0.9871443 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 13:53:01 rms-change max change #iterations 0.1520250 24.51090 at 10iterations 1.5600853E-02 2.311115 at 20iterations 1.7740343E-03 0.2175703 at 30iterations 3.1547691E-04 4.7012329E-02 at 40iterations 7.6468386E-05 1.2273788E-02 at 50iterations finished qdiffx linear iterations at : 13:53:05 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 7.6468386E-05 1.2273788E-02 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 13:53:05 4.473u 0.411s 0:05.21 93.6% 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 8 2011 at 13:53:05 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2970 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.902421 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): -11.50700 43.19900 ymin,ymax (A): 11.15700 55.00500 zmin,zma (A): 37.49100 93.63000 x,y,z range (A): 54.70600 43.84800 56.13900 scale (grids/A): 1.902421 object centre (A): 15.84600 33.08100 65.56050 number of atom coordinates read : 2970 total number of charged atoms : 2823 net assigned charge : -1.499993 assigned positive charge : 445.5066 centred at (gu) : 87.29002 88.41106 93.91528 assigned negative charge : -447.0074 centred at (gu) : 87.24004 88.15697 93.67473 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23271 grid for indexing accessible points = 1.400000 m= 32673 mr = 63382 m= 4815 mr = 24879 m= 228 mr = 2989 m= 0 mr = 69 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 530 time to turn everything in is 0.6900000 number of dielectric boundary points 33578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22242 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) : 0.6341402 object centre at (A) : 15.84600 33.08100 65.56050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5445422E-02 1.1899459E-02 midg,1,midg; midg,igrid,midg -3.3169384E-03 1.4320143E-02 1,midg,midg; igrid,midg,midg -4.5794267E-02 1.8672650E-03 gauss-seidel spectral radius is 0.9986611 estimated iterations to convergence 217 setup time was (sec) 1.030000 now iterating at: 13:53:07 rms-change max change #iterations 4.590967 165.6846 at 10iterations 2.175673 66.16145 at 20iterations 1.026527 30.38022 at 30iterations 0.4864959 15.18745 at 40iterations 0.2293119 6.397511 at 50iterations 0.1083336 3.043549 at 60iterations 5.1253613E-02 1.432523 at 70iterations 2.4240626E-02 0.7220764 at 80iterations 1.1564282E-02 0.3632164 at 90iterations 5.5245352E-03 0.1645987 at 100iterations 2.6448600E-03 8.0204010E-02 at 110iterations 1.2807255E-03 4.0225983E-02 at 120iterations finished qdiffx linear iterations at : 13:53:16 total time elapsed so far: 10.63000 # loops : 120 mean,max change (kT/e) : 1.2807255E-03 4.0225983E-02 energy calculations done at 10.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 13:53:17 10.807u 0.464s 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 Sat Oct 8 2011 at 13:53:17 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2970 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.853631 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): -11.50700 43.19900 ymin,ymax (A): 11.15700 55.00500 zmin,zma (A): 37.49100 93.63000 x,y,z range (A): 54.70600 43.84800 56.13900 scale (grids/A): 2.853631 object centre (A): 15.84600 33.08100 65.56050 number of atom coordinates read : 2970 total number of charged atoms : 2823 net assigned charge : -1.499993 assigned positive charge : 445.5066 centred at (gu) : 85.93482 87.61663 95.87280 assigned negative charge : -447.0074 centred at (gu) : 85.85999 87.23538 95.51209 start vw surface at 0.1300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 202134 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23271 grid for indexing accessible points = 1.400000 m= 106187 mr = 153308 m= 37889 mr = 88829 m= 8536 mr = 30900 m= 1083 mr = 6422 m= 43 mr = 697 m= 0 mr = 6 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 1569 time to turn everything in is 1.840000 number of dielectric boundary points 75710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 22584 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) : 1.902421 object centre at (A) : 15.84600 33.08100 65.56050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1118031 0.1330136 midg,1,midg; midg,igrid,midg -9.6308254E-03 0.1595043 1,midg,midg; igrid,midg,midg -0.7503592 0.1886985 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 2.180000 now iterating at: 13:53:20 rms-change max change #iterations 10.82599 332.7435 at 10iterations 6.404518 192.4561 at 20iterations 3.751950 76.07664 at 30iterations 2.190058 40.41537 at 40iterations 1.278688 29.15598 at 50iterations 0.7417662 14.22956 at 60iterations 0.4310677 8.272423 at 70iterations 0.2496792 5.754180 at 80iterations 0.1444296 2.677521 at 90iterations 8.3599016E-02 1.326584 at 100iterations 4.8376501E-02 0.7818680 at 110iterations 2.7980808E-02 0.5105095 at 120iterations 1.6210645E-02 0.2879181 at 130iterations 9.4113778E-03 0.1618118 at 140iterations 5.4709446E-03 8.7650299E-02 at 150iterations 3.2057355E-03 5.0125122E-02 at 160iterations 1.8985936E-03 3.3287048E-02 at 170iterations 1.1444751E-03 2.3700714E-02 at 180iterations finished qdiffx linear iterations at : 13:53:35 total time elapsed so far: 18.07000 # loops : 180 mean,max change (kT/e) : 1.1444751E-03 2.3700714E-02 energy calculations done at 18.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.24000 DelPhi exited at 13:53:36 18.242u 0.474s 0:19.01 98.4% 0+0k 0+0io 0pf+0w