Sun Oct 9 12:09:26 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 Sun Oct 9 2011 at 12:09:26 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 = 2396 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: 0.6853403 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): -6.661000 42.97100 ymin,ymax (A): -13.73800 38.20700 zmin,zma (A): 0.8500000 45.10000 x,y,z range (A): 49.63200 51.94500 44.25000 scale (grids/A): 0.6853403 object centre (A): 18.15500 12.23450 22.97500 number of atom coordinates read : 2396 total number of charged atoms : 2254 net assigned charge : 3.500023 assigned positive charge : 366.9480 centred at (gu) : 90.27990 91.00948 91.11809 assigned negative charge : -363.4486 centred at (gu) : 90.31301 91.14516 91.20624 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7573 nv = 96 ne = 84 npr = 48627 no. pairs analyzed = 48627 no. exposed pairs = 2992 no. arc points = 21058 no. surface atoms = 1016 nbur = 1380 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4203 m= 2 mr = 70 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 3787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2028 ## 206 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8659 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8682714E-08 -1.6082458E-08 midg,1,midg; midg,igrid,midg 5.2581790E-08 -3.6392819E-08 1,midg,midg; igrid,midg,midg 2.7993202E-08 7.0565100E-09 gauss-seidel spectral radius is 0.9889410 estimated iterations to convergence 78 setup time was (sec) 0.4800000 now iterating at: 12:09:27 rms-change max change #iterations 0.1855778 24.81575 at 10iterations 2.2005713E-02 3.043356 at 20iterations 2.8428438E-03 0.4265671 at 30iterations 4.8816568E-04 6.3652039E-02 at 40iterations 1.1761537E-04 1.4766693E-02 at 50iterations finished qdiffx linear iterations at : 12:09:29 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.1761537E-04 1.4766693E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 12:09:30 3.086u 0.137s 0:03.53 90.9% 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 12:09:30 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 = 2396 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: 2.056021 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): -6.661000 42.97100 ymin,ymax (A): -13.73800 38.20700 zmin,zma (A): 0.8500000 45.10000 x,y,z range (A): 49.63200 51.94500 44.25000 scale (grids/A): 2.056021 object centre (A): 18.15500 12.23450 22.97500 number of atom coordinates read : 2396 total number of charged atoms : 2254 net assigned charge : 3.500023 assigned positive charge : 366.9480 centred at (gu) : 90.83926 93.02785 93.35384 assigned negative charge : -363.4486 centred at (gu) : 90.93884 93.43509 93.61843 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21058 grid for indexing accessible points = 1.400000 m= 31583 mr = 55410 m= 5865 mr = 23751 m= 497 mr = 3745 m= 11 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 326 time to turn everything in is 0.5600000 number of dielectric boundary points 34791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17888 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) : 0.6853403 object centre at (A) : 18.15500 12.23450 22.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0473815E-02 4.3578008E-03 midg,1,midg; midg,igrid,midg 2.2920009E-02 -4.0169585E-02 1,midg,midg; igrid,midg,midg 3.9842632E-02 -2.4528250E-02 gauss-seidel spectral radius is 0.9988008 estimated iterations to convergence 229 setup time was (sec) 0.8200000 now iterating at: 12:09:31 rms-change max change #iterations 4.768112 234.2537 at 10iterations 2.328598 75.40016 at 20iterations 1.141523 35.89434 at 30iterations 0.5601049 16.68514 at 40iterations 0.2762321 9.516063 at 50iterations 0.1359043 4.004526 at 60iterations 6.6963911E-02 1.946785 at 70iterations 3.2955181E-02 1.005646 at 80iterations 1.6281653E-02 0.4939842 at 90iterations 8.0490215E-03 0.2298260 at 100iterations 4.0127276E-03 0.1231604 at 110iterations 2.0195604E-03 5.6030273E-02 at 120iterations finished qdiffx linear iterations at : 12:09:37 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 2.0195604E-03 5.6030273E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 12:09:37 6.924u 0.155s 0:07.39 95.6% 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 Sun Oct 9 2011 at 12:09:37 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 = 2396 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: 3.084031 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): -6.661000 42.97100 ymin,ymax (A): -13.73800 38.20700 zmin,zma (A): 0.8500000 45.10000 x,y,z range (A): 49.63200 51.94500 44.25000 scale (grids/A): 3.084031 object centre (A): 18.15500 12.23450 22.97500 number of atom coordinates read : 2396 total number of charged atoms : 2254 net assigned charge : 3.500023 assigned positive charge : 366.9480 centred at (gu) : 91.25880 94.54157 95.03064 assigned negative charge : -363.4486 centred at (gu) : 91.40824 95.15266 95.42757 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 184520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21058 grid for indexing accessible points = 1.400000 m= 98271 mr = 133837 m= 39749 mr = 81090 m= 11127 mr = 32622 m= 2022 mr = 8414 m= 214 mr = 1370 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1061 time to turn everything in is 1.770000 number of dielectric boundary points 78457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 18032 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) : 2.056021 object centre at (A) : 18.15500 12.23450 22.97500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3431601 -8.0754608E-02 midg,1,midg; midg,igrid,midg 0.4523236 -0.3506123 1,midg,midg; igrid,midg,midg 0.4380327 -0.5534207 gauss-seidel spectral radius is 0.9992915 estimated iterations to convergence 296 setup time was (sec) 2.050000 now iterating at: 12:09:39 rms-change max change #iterations 10.84839 428.7991 at 10iterations 6.463997 140.7622 at 20iterations 3.820731 70.15230 at 30iterations 2.255122 43.43050 at 40iterations 1.331914 27.44474 at 50iterations 0.7825453 14.98332 at 60iterations 0.4595309 7.996828 at 70iterations 0.2698170 4.735123 at 80iterations 0.1582503 2.898706 at 90iterations 9.2505641E-02 1.657339 at 100iterations 5.4133199E-02 1.042526 at 110iterations 3.1872898E-02 0.5303259 at 120iterations 1.8739915E-02 0.3296833 at 130iterations 1.1098712E-02 0.2138748 at 140iterations 6.6738632E-03 0.1278343 at 150iterations 4.0921862E-03 8.2443237E-02 at 160iterations 2.5928284E-03 5.3794861E-02 at 170iterations 1.7166765E-03 3.7334442E-02 at 180iterations finished qdiffx linear iterations at : 12:09:50 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 1.7166765E-03 3.7334442E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 12:09:50 12.416u 0.162s 0:12.84 97.8% 0+0k 0+0io 0pf+0w