Tue Oct 11 07:13:53 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 07:13:53 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: SEP 167 has a net charge of -0.4750 !!! WARNING: HIR 207 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6618207 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): -54.51600 -0.7250000 ymin,ymax (A): -28.42800 24.11500 zmin,zma (A): -1.763000 44.03900 x,y,z range (A): 53.79100 52.54300 45.80200 scale (grids/A): 0.6618207 object centre (A): -27.62050 -2.156500 21.13800 number of atom coordinates read : 2542 total number of charged atoms : 2397 net assigned charge : -4.054994 assigned positive charge : 376.5371 centred at (gu) : 90.06450 90.91521 88.54502 assigned negative charge : -380.5926 centred at (gu) : 89.93196 90.86179 88.40805 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7698 nv = 96 ne = 84 npr = 51490 no. pairs analyzed = 51490 no. exposed pairs = 3222 no. arc points = 22291 no. surface atoms = 1100 nbur = 1442 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 425 mr = 4351 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2068 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2428472E-08 1.2337585E-08 midg,1,midg; midg,igrid,midg -1.7672006E-08 5.4487342E-10 1,midg,midg; igrid,midg,midg -3.7162646E-08 1.6280110E-08 gauss-seidel spectral radius is 0.9881659 estimated iterations to convergence 75 setup time was (sec) 0.6800000 now iterating at: 07:13:54 rms-change max change #iterations 0.1673875 24.62889 at 10iterations 1.8424660E-02 2.816153 at 20iterations 2.0045501E-03 0.2954774 at 30iterations 2.6218558E-04 4.8576355E-02 at 40iterations 5.3622698E-05 9.9067688E-03 at 50iterations finished qdiffx linear iterations at : 07:13:57 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 5.3622698E-05 9.9067688E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 07:13:57 4.243u 0.198s 0:04.75 93.2% 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 07:13:57 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: SEP 167 has a net charge of -0.4750 !!! WARNING: HIR 207 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.985462 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): -54.51600 -0.7250000 ymin,ymax (A): -28.42800 24.11500 zmin,zma (A): -1.763000 44.03900 x,y,z range (A): 53.79100 52.54300 45.80200 scale (grids/A): 1.985462 object centre (A): -27.62050 -2.156500 21.13800 number of atom coordinates read : 2542 total number of charged atoms : 2397 net assigned charge : -4.054994 assigned positive charge : 376.5371 centred at (gu) : 90.19311 92.74520 85.63478 assigned negative charge : -380.5926 centred at (gu) : 89.79565 92.58508 85.22403 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 82045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22291 grid for indexing accessible points = 1.400000 m= 32042 mr = 57618 m= 5668 mr = 24441 m= 433 mr = 3810 m= 7 mr = 198 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 571 time to turn everything in is 0.7600000 number of dielectric boundary points 34128 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 18941 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) : 0.6618207 object centre at (A) : -27.62050 -2.156500 21.13800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7957397E-02 1.9551629E-02 midg,1,midg; midg,igrid,midg -3.8518660E-02 -4.1948486E-02 1,midg,midg; igrid,midg,midg -4.1311610E-02 -3.5555091E-02 gauss-seidel spectral radius is 0.9987381 estimated iterations to convergence 223 setup time was (sec) 1.120000 now iterating at: 07:13:59 rms-change max change #iterations 4.570675 190.7818 at 10iterations 2.216091 82.38374 at 20iterations 1.067366 36.71813 at 30iterations 0.5148081 16.17842 at 40iterations 0.2486586 6.877190 at 50iterations 0.1202651 3.551902 at 60iterations 5.8220673E-02 1.636128 at 70iterations 2.8154206E-02 0.8727474 at 80iterations 1.3573902E-02 0.4260149 at 90iterations 6.5659774E-03 0.1984978 at 100iterations 3.1852087E-03 0.1010404 at 110iterations 1.5553714E-03 4.8751831E-02 at 120iterations finished qdiffx linear iterations at : 07:14:07 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 1.5553714E-03 4.8751831E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 07:14:08 9.618u 0.235s 0:10.40 94.6% 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 Tue Oct 11 2011 at 07:14:08 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: SEP 167 has a net charge of -0.4750 !!! WARNING: HIR 207 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.978193 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): -54.51600 -0.7250000 ymin,ymax (A): -28.42800 24.11500 zmin,zma (A): -1.763000 44.03900 x,y,z range (A): 53.79100 52.54300 45.80200 scale (grids/A): 2.978193 object centre (A): -27.62050 -2.156500 21.13800 number of atom coordinates read : 2542 total number of charged atoms : 2397 net assigned charge : -4.054994 assigned positive charge : 376.5371 centred at (gu) : 90.28946 94.11773 83.45200 assigned negative charge : -380.5926 centred at (gu) : 89.69341 93.87743 82.83604 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 189489 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22291 grid for indexing accessible points = 1.400000 m= 100652 mr = 138844 m= 39744 mr = 83876 m= 10450 mr = 32967 m= 1794 mr = 8185 m= 129 mr = 1314 m= 3 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 1.190000 no. cavity mid-points inaccessible to solvent = 2007 time to turn everything in is 1.970000 number of dielectric boundary points 77017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 19176 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) : 1.985462 object centre at (A) : -27.62050 -2.156500 21.13800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4625042 0.1389148 midg,1,midg; midg,igrid,midg -0.5049488 -0.5832770 1,midg,midg; igrid,midg,midg -0.2678611 -0.4246610 gauss-seidel spectral radius is 0.9992875 estimated iterations to convergence 296 setup time was (sec) 2.350000 now iterating at: 07:14:10 rms-change max change #iterations 10.49896 463.9619 at 10iterations 6.163860 143.3180 at 20iterations 3.612624 73.17765 at 30iterations 2.111877 36.71014 at 40iterations 1.229309 23.28729 at 50iterations 0.7168268 14.32288 at 60iterations 0.4181459 7.503507 at 70iterations 0.2427613 4.222413 at 80iterations 0.1410012 2.667290 at 90iterations 8.2090631E-02 1.387768 at 100iterations 4.7618177E-02 0.8987923 at 110iterations 2.7637256E-02 0.4928513 at 120iterations 1.6055502E-02 0.2774346 at 130iterations 9.3336012E-03 0.1558261 at 140iterations 5.4400857E-03 9.1041565E-02 at 150iterations 3.1689501E-03 5.7455063E-02 at 160iterations 1.8627397E-03 3.3258438E-02 at 170iterations 1.1023969E-03 1.7749786E-02 at 180iterations finished qdiffx linear iterations at : 07:14:23 total time elapsed so far: 15.35000 # loops : 180 mean,max change (kT/e) : 1.1023969E-03 1.7749786E-02 energy calculations done at 15.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.59000 DelPhi exited at 07:14:24 15.591u 0.265s 0:16.32 97.1% 0+0k 0+0io 0pf+0w