Sat Oct 8 18:10:36 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 18:10:36 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 = 4699 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5096855 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): -1.136000 61.15200 ymin,ymax (A): -30.04800 30.78600 zmin,zma (A): -22.85000 46.99700 x,y,z range (A): 62.28800 60.83400 69.84700 scale (grids/A): 0.5096855 object centre (A): 30.00800 0.3689995 12.07350 number of atom coordinates read : 4699 total number of charged atoms : 4544 net assigned charge : -10.99997 assigned positive charge : 714.9670 centred at (gu) : 90.81469 91.17065 90.58700 assigned negative charge : -725.9720 centred at (gu) : 90.83222 91.13371 90.59415 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7882 nv = 96 ne = 84 npr = 92651 no. pairs analyzed = 92651 no. exposed pairs = 6182 no. arc points = 43528 no. surface atoms = 2058 nbur = 2641 mkacc time = 0.3100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 281 mr = 3883 m= 3 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 4272 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4309 ## 650 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 10551 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1386438E-10 -1.9594430E-10 midg,1,midg; midg,igrid,midg -1.8028783E-10 -7.5686263E-11 1,midg,midg; igrid,midg,midg -8.6433576E-11 -2.4071259E-10 gauss-seidel spectral radius is 0.9803210 estimated iterations to convergence 59 setup time was (sec) 0.9300000 now iterating at: 18:10:37 rms-change max change #iterations 6.3403584E-02 9.184731 at 10iterations 3.6175053E-03 0.5850077 at 20iterations 3.0919272E-04 4.6905518E-02 at 30iterations 5.5990098E-05 1.0023117E-02 at 40iterations 1.2898975E-05 2.2649765E-03 at 50iterations finished qdiffx linear iterations at : 18:10:41 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 1.2898975E-05 2.2649765E-03 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 18:10:41 4.754u 0.441s 0:05.49 94.5% 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 18:10:41 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 = 4699 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.529056 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): -1.136000 61.15200 ymin,ymax (A): -30.04800 30.78600 zmin,zma (A): -22.85000 46.99700 x,y,z range (A): 62.28800 60.83400 69.84700 scale (grids/A): 1.529056 object centre (A): 30.00800 0.3689995 12.07350 number of atom coordinates read : 4699 total number of charged atoms : 4544 net assigned charge : -10.99997 assigned positive charge : 714.9670 centred at (gu) : 92.44259 93.51035 91.75968 assigned negative charge : -725.9720 centred at (gu) : 92.49647 93.40083 91.78233 start vw surface at 0.2200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 88646 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43528 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25138 mr = 58978 m= 2149 mr = 16293 m= 48 mr = 856 m= 0 mr = 1 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 157 time to turn everything in is 0.9100000 number of dielectric boundary points 39853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 585 ## 9 charges are in solution ## iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 34104 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) : 0.5096855 object centre at (A) : 30.00800 0.3689995 12.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2359480E-03 -2.4209389E-02 midg,1,midg; midg,igrid,midg -1.4897130E-02 -8.5610673E-03 1,midg,midg; igrid,midg,midg 3.7716180E-03 -2.4051417E-03 gauss-seidel spectral radius is 0.9981044 estimated iterations to convergence 183 setup time was (sec) 1.230000 now iterating at: 18:10:43 rms-change max change #iterations 3.760615 157.4848 at 10iterations 1.532848 52.22559 at 20iterations 0.6264201 19.87565 at 30iterations 0.2562406 8.711946 at 40iterations 0.1048243 3.618431 at 50iterations 4.2771280E-02 1.382356 at 60iterations 1.7570637E-02 0.5461941 at 70iterations 7.1967086E-03 0.2533207 at 80iterations 2.9669947E-03 9.8947525E-02 at 90iterations 1.2216889E-03 3.9766312E-02 at 100iterations 5.1192596E-04 1.6092718E-02 at 110iterations 2.1739111E-04 7.4043274E-03 at 120iterations finished qdiffx linear iterations at : 18:10:52 total time elapsed so far: 10.47000 # loops : 120 mean,max change (kT/e) : 2.1739111E-04 7.4043274E-03 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.68000 DelPhi exited at 18:10:53 10.689u 0.489s 0:11.45 97.4% 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 Sat Oct 8 2011 at 18:10:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4699 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.293585 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): -1.136000 61.15200 ymin,ymax (A): -30.04800 30.78600 zmin,zma (A): -22.85000 46.99700 x,y,z range (A): 62.28800 60.83400 69.84700 scale (grids/A): 2.293585 object centre (A): 30.00800 0.3689995 12.07350 number of atom coordinates read : 4699 total number of charged atoms : 4544 net assigned charge : -10.99997 assigned positive charge : 714.9670 centred at (gu) : 93.66356 95.26523 92.63879 assigned negative charge : -725.9720 centred at (gu) : 93.74470 95.10114 92.67344 start vw surface at 0.2100000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 206319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43528 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90000 mr = 145067 m= 22311 mr = 69245 m= 3051 mr = 15765 m= 174 mr = 1705 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 525 time to turn everything in is 2.310000 number of dielectric boundary points 90027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 2.460000 number of grid points assigned charge 36250 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) : 1.529056 object centre at (A) : 30.00800 0.3689995 12.07350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2083113 -0.3218860 midg,1,midg; midg,igrid,midg -0.3644614 -0.1487661 1,midg,midg; igrid,midg,midg 4.7453083E-02 -9.1015145E-02 gauss-seidel spectral radius is 0.9991586 estimated iterations to convergence 272 setup time was (sec) 2.660000 now iterating at: 18:10:56 rms-change max change #iterations 10.31669 311.9675 at 10iterations 5.952420 160.4147 at 20iterations 3.399264 74.94687 at 30iterations 1.928840 38.40219 at 40iterations 1.087849 23.35423 at 50iterations 0.6113846 11.92873 at 60iterations 0.3426791 6.469669 at 70iterations 0.1914627 4.113731 at 80iterations 0.1069175 1.994227 at 90iterations 5.9574638E-02 1.104447 at 100iterations 3.3154819E-02 0.6718178 at 110iterations 1.8486261E-02 0.3951654 at 120iterations 1.0246998E-02 0.2076912 at 130iterations 5.6987074E-03 0.1075287 at 140iterations 3.1660099E-03 6.4412594E-02 at 150iterations 1.7574115E-03 3.3737183E-02 at 160iterations 9.7737438E-04 1.9508362E-02 at 170iterations 5.4356217E-04 9.6945763E-03 at 180iterations finished qdiffx linear iterations at : 18:11:12 total time elapsed so far: 18.32000 # loops : 180 mean,max change (kT/e) : 5.4356217E-04 9.6945763E-03 energy calculations done at 18.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.53000 DelPhi exited at 18:11:12 18.539u 0.521s 0:19.35 98.4% 0+0k 0+0io 0pf+0w