Sat Oct 8 23:36:29 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 23:36:29 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 = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6486408 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): 56.38000 99.50300 ymin,ymax (A): 30.75100 85.63500 zmin,zma (A): 25.99700 80.07500 x,y,z range (A): 43.12300 54.88400 54.07800 scale (grids/A): 0.6486408 object centre (A): 77.94150 58.19300 53.03600 number of atom coordinates read : 2451 total number of charged atoms : 2315 net assigned charge : 11.50002 assigned positive charge : 357.9943 centred at (gu) : 89.59309 89.11768 90.71580 assigned negative charge : -346.4950 centred at (gu) : 89.67303 89.18904 90.68003 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7131 nv = 96 ne = 84 npr = 48877 no. pairs analyzed = 48877 no. exposed pairs = 3189 no. arc points = 22298 no. surface atoms = 1081 nbur = 1370 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 436 mr = 3815 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2171 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8280 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4286174E-08 2.9998404E-08 midg,1,midg; midg,igrid,midg 3.6649158E-08 9.9100399E-09 1,midg,midg; igrid,midg,midg 3.4389814E-08 9.8141664E-09 gauss-seidel spectral radius is 0.9876783 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 23:36:29 rms-change max change #iterations 0.1459707 22.19145 at 10iterations 1.4770064E-02 2.203266 at 20iterations 1.5985045E-03 0.2351379 at 30iterations 2.3948138E-04 3.6735535E-02 at 40iterations 5.9095117E-05 1.0520935E-02 at 50iterations finished qdiffx linear iterations at : 23:36:32 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.9095117E-05 1.0520935E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 23:36:33 3.368u 0.173s 0:03.84 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 Sat Oct 8 2011 at 23:36:33 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 = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.945922 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): 56.38000 99.50300 ymin,ymax (A): 30.75100 85.63500 zmin,zma (A): 25.99700 80.07500 x,y,z range (A): 43.12300 54.88400 54.07800 scale (grids/A): 1.945922 object centre (A): 77.94150 58.19300 53.03600 number of atom coordinates read : 2451 total number of charged atoms : 2315 net assigned charge : 11.50002 assigned positive charge : 357.9943 centred at (gu) : 88.77882 87.35263 92.14726 assigned negative charge : -346.4950 centred at (gu) : 89.01886 87.56714 92.03989 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75689 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 29291 mr = 51517 m= 5356 mr = 21850 m= 379 mr = 3506 m= 3 mr = 173 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 0.3800000 number of dielectric boundary points 33672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 18297 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) : 0.6486408 object centre at (A) : 77.94150 58.19300 53.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1970471E-02 5.6209218E-02 midg,1,midg; midg,igrid,midg 3.9891377E-02 5.8784682E-02 1,midg,midg; igrid,midg,midg 2.7091978E-02 7.1733412E-03 gauss-seidel spectral radius is 0.9986845 estimated iterations to convergence 218 setup time was (sec) 0.5800000 now iterating at: 23:36:33 rms-change max change #iterations 4.136044 249.2869 at 10iterations 1.960830 74.45784 at 20iterations 0.9300485 36.16837 at 30iterations 0.4411450 14.12968 at 40iterations 0.2098850 6.741951 at 50iterations 9.9531062E-02 3.308099 at 60iterations 4.7283668E-02 1.463295 at 70iterations 2.2476226E-02 0.7299004 at 80iterations 1.0722291E-02 0.3505010 at 90iterations 5.1332992E-03 0.2007084 at 100iterations 2.4574632E-03 7.2425842E-02 at 110iterations 1.2029451E-03 3.9531112E-02 at 120iterations finished qdiffx linear iterations at : 23:36:40 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.2029451E-03 3.9531112E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 23:36:41 7.769u 0.212s 0:08.28 96.2% 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 23:36:41 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 = 2451 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.918883 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): 56.38000 99.50300 ymin,ymax (A): 30.75100 85.63500 zmin,zma (A): 25.99700 80.07500 x,y,z range (A): 43.12300 54.88400 54.07800 scale (grids/A): 2.918883 object centre (A): 77.94150 58.19300 53.03600 number of atom coordinates read : 2451 total number of charged atoms : 2315 net assigned charge : 11.50002 assigned positive charge : 357.9943 centred at (gu) : 88.16819 86.02882 93.22079 assigned negative charge : -346.4950 centred at (gu) : 88.52827 86.35075 93.05969 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 174202 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22298 grid for indexing accessible points = 1.400000 m= 91080 mr = 124477 m= 36860 mr = 74551 m= 9931 mr = 30124 m= 1623 mr = 7636 m= 146 mr = 1165 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 75797 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 18519 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) : 1.945922 object centre at (A) : 77.94150 58.19300 53.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3154415 0.4633421 midg,1,midg; midg,igrid,midg 0.4101125 0.7689530 1,midg,midg; igrid,midg,midg 0.2324626 7.3127702E-02 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.230000 now iterating at: 23:36:42 rms-change max change #iterations 9.775895 428.2010 at 10iterations 5.783428 144.1156 at 20iterations 3.409884 77.31833 at 30iterations 1.994951 41.83006 at 40iterations 1.165557 23.12652 at 50iterations 0.6804169 14.70111 at 60iterations 0.3977914 7.564522 at 70iterations 0.2308773 4.154402 at 80iterations 0.1342060 2.646720 at 90iterations 7.7957876E-02 1.517720 at 100iterations 4.5244776E-02 0.8721590 at 110iterations 2.6283687E-02 0.4832306 at 120iterations 1.5227980E-02 0.2844906 at 130iterations 8.8385120E-03 0.1578884 at 140iterations 5.1214034E-03 9.4420433E-02 at 150iterations 2.9746385E-03 5.6468964E-02 at 160iterations 1.7321664E-03 3.2419205E-02 at 170iterations 1.0130595E-03 1.9214630E-02 at 180iterations finished qdiffx linear iterations at : 23:36:54 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.0130595E-03 1.9214630E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 23:36:54 12.816u 0.206s 0:13.29 97.8% 0+0k 0+0io 0pf+0w