Tue Oct 11 03:20:58 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 03:20:58 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 !!! WARNING: GLM 12 has a net charge of -0.0940 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: 0.5367346 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): 60.10600 109.9180 ymin,ymax (A): -3.203000 56.13700 zmin,zma (A): 35.89300 102.2200 x,y,z range (A): 49.81200 59.34000 66.32700 scale (grids/A): 0.5367346 object centre (A): 85.01200 26.46700 69.05650 number of atom coordinates read : 3199 total number of charged atoms : 3056 net assigned charge : -6.093974 assigned positive charge : 480.8907 centred at (gu) : 88.98045 91.60902 92.87419 assigned negative charge : -486.9858 centred at (gu) : 89.02128 91.60142 92.90322 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5777 nv = 96 ne = 84 npr = 66617 no. pairs analyzed = 66617 no. exposed pairs = 3965 no. arc points = 27158 no. surface atoms = 1343 nbur = 1856 mkacc time = 0.1700000 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 = 1.596000 m= 214 mr = 3002 m= 1 mr = 9 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 0.3700000 number of dielectric boundary points 2981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 389 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 7748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8144933E-11 -8.3436530E-10 midg,1,midg; midg,igrid,midg -1.9967429E-10 -3.2377945E-10 1,midg,midg; igrid,midg,midg -6.3856753E-11 -3.6026249E-10 gauss-seidel spectral radius is 0.9821216 estimated iterations to convergence 62 setup time was (sec) 0.7100000 now iterating at: 03:20:59 rms-change max change #iterations 7.1272910E-02 12.41784 at 10iterations 4.5988434E-03 0.8127394 at 20iterations 3.5681317E-04 6.7818642E-02 at 30iterations 4.0103881E-05 7.1463585E-03 at 40iterations 6.7413162E-06 1.3234615E-03 at 50iterations finished qdiffx linear iterations at : 03:21:03 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 6.7413162E-06 1.3234615E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 03:21:04 4.772u 0.403s 0:05.68 91.0% 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 03:21:04 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 !!! WARNING: GLM 12 has a net charge of -0.0940 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: 1.610204 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): 60.10600 109.9180 ymin,ymax (A): -3.203000 56.13700 zmin,zma (A): 35.89300 102.2200 x,y,z range (A): 49.81200 59.34000 66.32700 scale (grids/A): 1.610204 object centre (A): 85.01200 26.46700 69.05650 number of atom coordinates read : 3199 total number of charged atoms : 3056 net assigned charge : -6.093974 assigned positive charge : 480.8907 centred at (gu) : 86.94071 94.82610 98.62160 assigned negative charge : -486.9858 centred at (gu) : 87.06350 94.80393 98.70950 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 64225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 19286 mr = 43488 m= 1975 mr = 13351 m= 37 mr = 966 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.5300000 number of dielectric boundary points 27716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23268 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) : 0.5367346 object centre at (A) : 85.01200 26.46700 69.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3944460E-02 -1.3188769E-02 midg,1,midg; midg,igrid,midg -3.2738768E-03 3.6682414E-03 1,midg,midg; igrid,midg,midg -3.3018505E-03 -6.3315239E-03 gauss-seidel spectral radius is 0.9981383 estimated iterations to convergence 184 setup time was (sec) 0.8800000 now iterating at: 03:21:05 rms-change max change #iterations 3.381249 156.8327 at 10iterations 1.387717 57.07169 at 20iterations 0.5715715 28.27423 at 30iterations 0.2357134 9.176060 at 40iterations 9.7651958E-02 3.561152 at 50iterations 4.0127605E-02 1.454817 at 60iterations 1.6615640E-02 0.5798874 at 70iterations 6.8424190E-03 0.2519703 at 80iterations 2.8415718E-03 0.1054831 at 90iterations 1.1815736E-03 4.1374207E-02 at 100iterations 4.9301598E-04 1.6021729E-02 at 110iterations 2.0981148E-04 8.1796646E-03 at 120iterations finished qdiffx linear iterations at : 03:21:15 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 2.0981148E-04 8.1796646E-03 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 03:21:15 10.474u 0.469s 0:11.26 97.0% 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 03:21:15 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 !!! WARNING: GLM 12 has a net charge of -0.0940 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: 2.415306 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): 60.10600 109.9180 ymin,ymax (A): -3.203000 56.13700 zmin,zma (A): 35.89300 102.2200 x,y,z range (A): 49.81200 59.34000 66.32700 scale (grids/A): 2.415306 object centre (A): 85.01200 26.46700 69.05650 number of atom coordinates read : 3199 total number of charged atoms : 3056 net assigned charge : -6.093974 assigned positive charge : 480.8907 centred at (gu) : 85.41077 97.23911 102.9321 assigned negative charge : -486.9858 centred at (gu) : 85.59513 97.20586 103.0640 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 149294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27158 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67598 mr = 106454 m= 18681 mr = 53606 m= 2971 mr = 14180 m= 201 mr = 1959 m= 1 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 278 time to turn everything in is 1.300000 number of dielectric boundary points 62466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 24422 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) : 1.610204 object centre at (A) : 85.01200 26.46700 69.05650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4360428 -0.3310067 midg,1,midg; midg,igrid,midg 3.8192444E-03 0.1629867 1,midg,midg; igrid,midg,midg -4.1569736E-02 -8.4454514E-02 gauss-seidel spectral radius is 0.9991240 estimated iterations to convergence 267 setup time was (sec) 1.630000 now iterating at: 03:21:17 rms-change max change #iterations 8.828754 269.1547 at 10iterations 4.933609 132.9125 at 20iterations 2.744526 60.20163 at 30iterations 1.520875 34.03688 at 40iterations 0.8366338 18.29778 at 50iterations 0.4614645 10.08339 at 60iterations 0.2536528 5.480364 at 70iterations 0.1391006 3.022984 at 80iterations 7.6309107E-02 1.653000 at 90iterations 4.1694682E-02 0.8284435 at 100iterations 2.2863394E-02 0.5174885 at 110iterations 1.2529594E-02 0.2648878 at 120iterations 6.8618851E-03 0.1470337 at 130iterations 3.7507485E-03 7.4752808E-02 at 140iterations 2.0607775E-03 4.7250748E-02 at 150iterations 1.1278281E-03 2.3237228E-02 at 160iterations 6.1997777E-04 1.3128281E-02 at 170iterations 3.4171730E-04 7.3633194E-03 at 180iterations finished qdiffx linear iterations at : 03:21:33 total time elapsed so far: 17.48000 # loops : 180 mean,max change (kT/e) : 3.4171730E-04 7.3633194E-03 energy calculations done at 17.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.65000 DelPhi exited at 03:21:34 17.652u 0.482s 0:18.41 98.4% 0+0k 0+0io 0pf+0w