Mon Oct 10 14:37:52 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 Mon Oct 10 2011 at 14:37:52 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: GLU 317 has a net charge of -0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5884882 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): -23.27500 28.53600 ymin,ymax (A): -23.92700 36.56700 zmin,zma (A): -14.34100 36.94300 x,y,z range (A): 51.81100 60.49400 51.28400 scale (grids/A): 0.5884882 object centre (A): 2.630501 6.319999 11.30100 number of atom coordinates read : 2622 total number of charged atoms : 2462 net assigned charge : -0.4999926 assigned positive charge : 386.4829 centred at (gu) : 90.05552 90.79279 90.38990 assigned negative charge : -386.9834 centred at (gu) : 90.25301 90.67187 90.32882 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5981 nv = 96 ne = 84 npr = 52906 no. pairs analyzed = 52906 no. exposed pairs = 3485 no. arc points = 24471 no. surface atoms = 1180 nbur = 1442 mkacc time = 0.1200000 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 = 1.456000 m= 286 mr = 3028 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2430 ## 272 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5748249E-09 1.4971209E-09 midg,1,midg; midg,igrid,midg -2.7178850E-09 3.4347847E-09 1,midg,midg; igrid,midg,midg 4.6510369E-09 -5.3520037E-09 gauss-seidel spectral radius is 0.9850661 estimated iterations to convergence 67 setup time was (sec) 0.5000000 now iterating at: 14:37:53 rms-change max change #iterations 9.6093312E-02 16.46215 at 10iterations 7.7829366E-03 1.284843 at 20iterations 6.2506658E-04 0.1031580 at 30iterations 5.0521423E-05 9.8800659E-03 at 40iterations 4.1242724E-06 5.9318542E-04 at 50iterations finished qdiffx linear iterations at : 14:37:55 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 4.1242724E-06 5.9318542E-04 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:37:55 3.067u 0.138s 0:03.54 90.1% 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 Mon Oct 10 2011 at 14:37:55 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: GLU 317 has a net charge of -0.5000 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: 1.765464 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): -23.27500 28.53600 ymin,ymax (A): -23.92700 36.56700 zmin,zma (A): -14.34100 36.94300 x,y,z range (A): 51.81100 60.49400 51.28400 scale (grids/A): 1.765464 object centre (A): 2.630501 6.319999 11.30100 number of atom coordinates read : 2622 total number of charged atoms : 2462 net assigned charge : -0.4999926 assigned positive charge : 386.4829 centred at (gu) : 90.16629 92.37776 91.16904 assigned negative charge : -386.9834 centred at (gu) : 90.75873 92.01529 90.98625 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24471 grid for indexing accessible points = 1.400000 m= 20884 mr = 43650 m= 2522 mr = 14302 m= 93 mr = 1163 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 29801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 229 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19164 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) : 0.5884882 object centre at (A) : 2.630501 6.319999 11.30100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4492818E-03 -6.7732837E-03 midg,1,midg; midg,igrid,midg 4.5285243E-04 8.0452198E-03 1,midg,midg; igrid,midg,midg 6.6899420E-03 -2.9184062E-02 gauss-seidel spectral radius is 0.9984198 estimated iterations to convergence 200 setup time was (sec) 0.7100000 now iterating at: 14:37:56 rms-change max change #iterations 3.603463 185.9871 at 10iterations 1.578811 62.25033 at 20iterations 0.6975086 27.45703 at 30iterations 0.3079886 11.09616 at 40iterations 0.1360174 4.612727 at 50iterations 5.9967957E-02 2.140625 at 60iterations 2.6601290E-02 0.9588051 at 70iterations 1.1733660E-02 0.3908005 at 80iterations 5.2014799E-03 0.1802258 at 90iterations 2.2894873E-03 7.9917908E-02 at 100iterations 1.0116657E-03 4.2020798E-02 at 110iterations 4.4736086E-04 1.7452240E-02 at 120iterations finished qdiffx linear iterations at : 14:38:03 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 4.4736086E-04 1.7452240E-02 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 14:38:03 7.298u 0.181s 0:07.94 94.0% 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 Mon Oct 10 2011 at 14:38:03 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2622 !!! WARNING: GLU 317 has a net charge of -0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.648197 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): -23.27500 28.53600 ymin,ymax (A): -23.92700 36.56700 zmin,zma (A): -14.34100 36.94300 x,y,z range (A): 51.81100 60.49400 51.28400 scale (grids/A): 2.648197 object centre (A): 2.630501 6.319999 11.30100 number of atom coordinates read : 2622 total number of charged atoms : 2462 net assigned charge : -0.4999926 assigned positive charge : 386.4829 centred at (gu) : 90.24910 93.56657 91.75341 assigned negative charge : -386.9834 centred at (gu) : 91.13799 93.02293 91.47932 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 151459 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24471 grid for indexing accessible points = 1.400000 m= 70636 mr = 106509 m= 21973 mr = 55792 m= 3906 mr = 16338 m= 393 mr = 2466 m= 11 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 67078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 19683 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) : 1.765464 object centre at (A) : 2.630501 6.319999 11.30100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2524067E-02 -0.1722239 midg,1,midg; midg,igrid,midg 7.9907261E-02 2.3097912E-02 1,midg,midg; igrid,midg,midg 4.8924666E-02 -0.3791800 gauss-seidel spectral radius is 0.9992043 estimated iterations to convergence 280 setup time was (sec) 1.400000 now iterating at: 14:38:05 rms-change max change #iterations 9.020594 280.7726 at 10iterations 5.235671 116.2991 at 20iterations 2.988477 70.65150 at 30iterations 1.700693 36.95685 at 40iterations 0.9685637 21.85443 at 50iterations 0.5493734 12.86624 at 60iterations 0.3103420 7.096658 at 70iterations 0.1755060 3.483095 at 80iterations 9.9023588E-02 1.963489 at 90iterations 5.5792119E-02 1.268007 at 100iterations 3.1451505E-02 0.7083992 at 110iterations 1.7740242E-02 0.3489017 at 120iterations 9.9799782E-03 0.2065673 at 130iterations 5.6257024E-03 0.1079087 at 140iterations 3.1600690E-03 7.3070526E-02 at 150iterations 1.7775820E-03 3.8507462E-02 at 160iterations 9.9962158E-04 2.5314331E-02 at 170iterations 5.6327577E-04 1.2081623E-02 at 180iterations finished qdiffx linear iterations at : 14:38:14 total time elapsed so far: 10.61000 # loops : 180 mean,max change (kT/e) : 5.6327577E-04 1.2081623E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 14:38:15 10.794u 0.178s 0:11.75 93.2% 0+0k 0+0io 0pf+0w