Tue Oct 11 03:48:32 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 03:48:32 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: TYS 279 has a net charge of -0.6490 !!! WARNING: HIR 351 has a net charge of 0.5140 !!! WARNING: SEP 505 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 !!! WARNING: TYS 2 has a net charge of -0.3380 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: 0.6783019 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): 3.675000 56.15900 ymin,ymax (A): 17.84600 69.59299 zmin,zma (A): 20.73000 73.17800 x,y,z range (A): 52.48400 51.74699 52.44800 scale (grids/A): 0.6783019 object centre (A): 29.91700 43.71950 46.95400 number of atom coordinates read : 2747 total number of charged atoms : 2594 net assigned charge : 3.714020 assigned positive charge : 414.1819 centred at (gu) : 89.35867 89.59748 89.37506 assigned negative charge : -410.4685 centred at (gu) : 89.63126 89.62264 89.52770 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8603 nv = 96 ne = 84 npr = 56003 no. pairs analyzed = 56003 no. exposed pairs = 3384 no. arc points = 23588 no. surface atoms = 1139 nbur = 1608 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4940 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3100000 number of dielectric boundary points 4088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2243 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2809478E-08 -3.2240511E-08 midg,1,midg; midg,igrid,midg 2.4611595E-08 5.6690976E-09 1,midg,midg; igrid,midg,midg 1.1637028E-07 -6.8388616E-08 gauss-seidel spectral radius is 0.9887442 estimated iterations to convergence 77 setup time was (sec) 0.5500000 now iterating at: 03:48:32 rms-change max change #iterations 0.1988437 27.18587 at 10iterations 2.2285765E-02 2.932386 at 20iterations 2.5770462E-03 0.3269978 at 30iterations 3.0915884E-04 4.2945862E-02 at 40iterations 4.3957894E-05 5.7373047E-03 at 50iterations finished qdiffx linear iterations at : 03:48:35 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 4.3957894E-05 5.7373047E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:48:36 3.387u 0.178s 0:04.10 86.5% 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 Tue Oct 11 2011 at 03:48:36 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: TYS 279 has a net charge of -0.6490 !!! WARNING: HIR 351 has a net charge of 0.5140 !!! WARNING: SEP 505 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 !!! WARNING: TYS 2 has a net charge of -0.3380 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: 2.034906 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): 3.675000 56.15900 ymin,ymax (A): 17.84600 69.59299 zmin,zma (A): 20.73000 73.17800 x,y,z range (A): 52.48400 51.74699 52.44800 scale (grids/A): 2.034906 object centre (A): 29.91700 43.71950 46.95400 number of atom coordinates read : 2747 total number of charged atoms : 2594 net assigned charge : 3.714020 assigned positive charge : 414.1819 centred at (gu) : 88.07533 88.79197 88.12464 assigned negative charge : -410.4685 centred at (gu) : 88.89336 88.86759 88.58270 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 91133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23588 grid for indexing accessible points = 1.400000 m= 36685 mr = 64668 m= 6932 mr = 28151 m= 557 mr = 4723 m= 9 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1635 time to turn everything in is 0.6500000 number of dielectric boundary points 37518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20507 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) : 0.6783019 object centre at (A) : 29.91700 43.71950 46.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5590248E-02 -2.7888650E-02 midg,1,midg; midg,igrid,midg 3.2648932E-02 -5.2675074E-03 1,midg,midg; igrid,midg,midg 4.9191132E-02 -1.5884137E-02 gauss-seidel spectral radius is 0.9988098 estimated iterations to convergence 229 setup time was (sec) 0.9500000 now iterating at: 03:48:37 rms-change max change #iterations 5.042759 266.2511 at 10iterations 2.472586 83.92130 at 20iterations 1.214372 35.77835 at 30iterations 0.6006356 17.52027 at 40iterations 0.2963957 8.330933 at 50iterations 0.1462889 4.529711 at 60iterations 7.1941637E-02 1.953802 at 70iterations 3.5603765E-02 1.055185 at 80iterations 1.7471099E-02 0.4663830 at 90iterations 8.6367587E-03 0.2888527 at 100iterations 4.2545432E-03 0.1208801 at 110iterations 2.1058139E-03 6.3915253E-02 at 120iterations finished qdiffx linear iterations at : 03:48:44 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 2.1058139E-03 6.3915253E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 03:48:44 7.770u 0.224s 0:08.41 95.0% 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 03:48:44 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: TYS 279 has a net charge of -0.6490 !!! WARNING: HIR 351 has a net charge of 0.5140 !!! WARNING: SEP 505 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 !!! WARNING: TYS 2 has a net charge of -0.3380 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: 3.052359 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): 3.675000 56.15900 ymin,ymax (A): 17.84600 69.59299 zmin,zma (A): 20.73000 73.17800 x,y,z range (A): 52.48400 51.74699 52.44800 scale (grids/A): 3.052359 object centre (A): 29.91700 43.71950 46.95400 number of atom coordinates read : 2747 total number of charged atoms : 2594 net assigned charge : 3.714020 assigned positive charge : 414.1819 centred at (gu) : 87.11300 88.18793 87.18695 assigned negative charge : -410.4685 centred at (gu) : 88.34013 88.30138 87.87398 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 210138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23588 grid for indexing accessible points = 1.400000 m= 114024 mr = 155398 m= 47015 mr = 95490 m= 13168 mr = 39223 m= 2363 mr = 10295 m= 213 mr = 1739 m= 3 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 5179 time to turn everything in is 1.710000 number of dielectric boundary points 84676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 20738 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) : 2.034906 object centre at (A) : 29.91700 43.71950 46.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3613390 -0.3813475 midg,1,midg; midg,igrid,midg 0.2741175 -0.1898263 1,midg,midg; igrid,midg,midg 0.1350604 -2.3589902E-02 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 2.030000 now iterating at: 03:48:47 rms-change max change #iterations 11.23618 509.7607 at 10iterations 6.611528 126.1739 at 20iterations 3.891485 79.61677 at 30iterations 2.287148 39.87520 at 40iterations 1.346846 28.51294 at 50iterations 0.7900312 12.77902 at 60iterations 0.4634766 7.691339 at 70iterations 0.2714308 4.708691 at 80iterations 0.1589372 2.793727 at 90iterations 9.3048066E-02 1.439375 at 100iterations 5.4630570E-02 0.9605251 at 110iterations 3.1944659E-02 0.5142365 at 120iterations 1.8742526E-02 0.3258629 at 130iterations 1.0997880E-02 0.1798973 at 140iterations 6.4533809E-03 0.1070919 at 150iterations 3.8012010E-03 6.2341690E-02 at 160iterations 2.2589765E-03 3.4477234E-02 at 170iterations 1.3549327E-03 2.3138046E-02 at 180iterations finished qdiffx linear iterations at : 03:48:57 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 1.3549327E-03 2.3138046E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 03:48:58 12.904u 0.215s 0:13.41 97.7% 0+0k 0+0io 0pf+0w