Tue Oct 11 06:03:49 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 Tue Oct 11 2011 at 06:03:49 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7374723 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): -18.43900 29.83400 ymin,ymax (A): -11.72700 30.68900 zmin,zma (A): -8.507999 37.97400 x,y,z range (A): 48.27300 42.41600 46.48200 scale (grids/A): 0.7374723 object centre (A): 5.697500 9.481001 14.73300 number of atom coordinates read : 2036 total number of charged atoms : 1934 net assigned charge : 6.039010 assigned positive charge : 315.8980 centred at (gu) : 90.31256 89.80138 91.04731 assigned negative charge : -309.8592 centred at (gu) : 90.23708 89.71465 90.93116 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7666 nv = 96 ne = 84 npr = 40101 no. pairs analyzed = 40101 no. exposed pairs = 2524 no. arc points = 17134 no. surface atoms = 860 nbur = 1176 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 569 mr = 4458 m= 4 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1541 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8184 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2964861E-09 2.5165087E-07 midg,1,midg; midg,igrid,midg 1.8264458E-08 1.7324393E-07 1,midg,midg; igrid,midg,midg 2.7179109E-08 1.7954957E-07 gauss-seidel spectral radius is 0.9904054 estimated iterations to convergence 83 setup time was (sec) 0.3800000 now iterating at: 06:03:50 rms-change max change #iterations 0.2411710 39.51867 at 10iterations 3.2420963E-02 4.135529 at 20iterations 4.6450319E-03 0.6938782 at 30iterations 7.7507505E-04 0.1014099 at 40iterations 1.8669404E-04 2.3241043E-02 at 50iterations finished qdiffx linear iterations at : 06:03:53 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.8669404E-04 2.3241043E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 06:03:53 3.464u 0.172s 0:04.28 84.8% 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 Tue Oct 11 2011 at 06:03:53 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.212417 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): -18.43900 29.83400 ymin,ymax (A): -11.72700 30.68900 zmin,zma (A): -8.507999 37.97400 x,y,z range (A): 48.27300 42.41600 46.48200 scale (grids/A): 2.212417 object centre (A): 5.697500 9.481001 14.73300 number of atom coordinates read : 2036 total number of charged atoms : 1934 net assigned charge : 6.039010 assigned positive charge : 315.8980 centred at (gu) : 90.93780 89.40395 93.14189 assigned negative charge : -309.8592 centred at (gu) : 90.71157 89.14403 92.79358 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17134 grid for indexing accessible points = 1.400000 m= 34287 mr = 57593 m= 7347 mr = 26443 m= 742 mr = 5075 m= 24 mr = 403 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 33330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15380 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) : 0.7374723 object centre at (A) : 5.697500 9.481001 14.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0674088E-02 4.5194995E-02 midg,1,midg; midg,igrid,midg 2.9289752E-02 2.8179314E-02 1,midg,midg; igrid,midg,midg 4.2753402E-02 4.4728234E-02 gauss-seidel spectral radius is 0.9989081 estimated iterations to convergence 239 setup time was (sec) 0.6300000 now iterating at: 06:03:54 rms-change max change #iterations 4.952084 215.9774 at 10iterations 2.506310 96.91280 at 20iterations 1.277542 38.63118 at 30iterations 0.6494214 19.80571 at 40iterations 0.3290179 10.05411 at 50iterations 0.1674345 4.707952 at 60iterations 8.5013255E-02 2.709320 at 70iterations 4.3524414E-02 1.200569 at 80iterations 2.2235425E-02 0.6206512 at 90iterations 1.1406210E-02 0.3318852 at 100iterations 5.8836248E-03 0.1903992 at 110iterations 3.1087499E-03 9.1793060E-02 at 120iterations finished qdiffx linear iterations at : 06:04:01 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 3.1087499E-03 9.1793060E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 06:04:02 8.019u 0.216s 0:08.62 95.3% 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 Tue Oct 11 2011 at 06:04:02 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2036 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.318625 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): -18.43900 29.83400 ymin,ymax (A): -11.72700 30.68900 zmin,zma (A): -8.507999 37.97400 x,y,z range (A): 48.27300 42.41600 46.48200 scale (grids/A): 3.318625 object centre (A): 5.697500 9.481001 14.73300 number of atom coordinates read : 2036 total number of charged atoms : 1934 net assigned charge : 6.039010 assigned positive charge : 315.8980 centred at (gu) : 91.40672 89.10604 94.71297 assigned negative charge : -309.8592 centred at (gu) : 91.06731 88.71614 94.19025 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 185309 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17134 grid for indexing accessible points = 1.400000 m= 104284 mr = 138154 m= 45302 mr = 87675 m= 14089 mr = 37689 m= 3073 mr = 11134 m= 395 mr = 2308 m= 23 mr = 273 m= 0 mr = 9 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 75233 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 15472 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) : 2.212417 object centre at (A) : 5.697500 9.481001 14.73300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5467038 0.4341082 midg,1,midg; midg,igrid,midg 0.2462306 0.1301655 1,midg,midg; igrid,midg,midg 0.2465030 0.2734370 gauss-seidel spectral radius is 0.9993171 estimated iterations to convergence 302 setup time was (sec) 1.520000 now iterating at: 06:04:04 rms-change max change #iterations 10.87851 318.4567 at 10iterations 6.496644 138.9455 at 20iterations 3.860242 72.25368 at 30iterations 2.297667 43.90935 at 40iterations 1.363710 24.32433 at 50iterations 0.8078995 15.68640 at 60iterations 0.4786436 8.498894 at 70iterations 0.2828023 5.491543 at 80iterations 0.1671146 2.845743 at 90iterations 9.8994046E-02 1.948437 at 100iterations 5.8653325E-02 0.9854546 at 110iterations 3.5011686E-02 0.5517781 at 120iterations 2.0994937E-02 0.3495331 at 130iterations 1.2797455E-02 0.2290764 at 140iterations 8.0414023E-03 0.1425133 at 150iterations 5.2855057E-03 0.1008987 at 160iterations 3.6562961E-03 6.7043304E-02 at 170iterations 2.7001100E-03 4.9209595E-02 at 180iterations finished qdiffx linear iterations at : 06:04:15 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 2.7001100E-03 4.9209595E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 06:04:16 12.964u 0.231s 0:13.60 96.9% 0+0k 0+0io 0pf+0w