Tue Oct 11 03:48:59 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 03:48:59 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6525405 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): -10.96700 36.50500 ymin,ymax (A): -27.01700 21.72400 zmin,zma (A): -9.001000 45.55500 x,y,z range (A): 47.47200 48.74100 54.55600 scale (grids/A): 0.6525405 object centre (A): 12.76900 -2.646501 18.27700 number of atom coordinates read : 2833 total number of charged atoms : 2667 net assigned charge : 0.1130212 assigned positive charge : 429.6897 centred at (gu) : 89.87564 90.60382 91.35380 assigned negative charge : -429.5771 centred at (gu) : 89.60510 90.48328 91.28485 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8093 nv = 96 ne = 84 npr = 56939 no. pairs analyzed = 56939 no. exposed pairs = 3495 no. arc points = 24492 no. surface atoms = 1174 nbur = 1659 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4613 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3200000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2266 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9490 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3356194E-09 1.6601609E-08 midg,1,midg; midg,igrid,midg -1.9284490E-08 2.4482580E-08 1,midg,midg; igrid,midg,midg -5.1495864E-08 4.6176655E-08 gauss-seidel spectral radius is 0.9878489 estimated iterations to convergence 74 setup time was (sec) 0.5400000 now iterating at: 03:49:00 rms-change max change #iterations 0.1698693 23.09061 at 10iterations 1.8055828E-02 2.456778 at 20iterations 2.0827800E-03 0.2610588 at 30iterations 3.1676647E-04 4.6249390E-02 at 40iterations 7.5875098E-05 9.7389221E-03 at 50iterations finished qdiffx linear iterations at : 03:49:02 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 7.5875098E-05 9.7389221E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 03:49:03 3.223u 0.160s 0:03.92 86.2% 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 03:49:03 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 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: 1.957622 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): -10.96700 36.50500 ymin,ymax (A): -27.01700 21.72400 zmin,zma (A): -9.001000 45.55500 x,y,z range (A): 47.47200 48.74100 54.55600 scale (grids/A): 1.957622 object centre (A): 12.76900 -2.646501 18.27700 number of atom coordinates read : 2833 total number of charged atoms : 2667 net assigned charge : 0.1130212 assigned positive charge : 429.6897 centred at (gu) : 89.62638 91.81123 94.06084 assigned negative charge : -429.5771 centred at (gu) : 88.81483 91.44939 93.85409 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24492 grid for indexing accessible points = 1.400000 m= 33087 mr = 60842 m= 5583 mr = 25157 m= 338 mr = 3681 m= 5 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2442 time to turn everything in is 0.5900000 number of dielectric boundary points 35743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21061 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) : 0.6525405 object centre at (A) : 12.76900 -2.646501 18.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8094649E-02 5.8841575E-03 midg,1,midg; midg,igrid,midg -1.9152220E-02 3.5597095E-03 1,midg,midg; igrid,midg,midg -1.7008446E-02 6.0888708E-02 gauss-seidel spectral radius is 0.9987305 estimated iterations to convergence 222 setup time was (sec) 0.8600000 now iterating at: 03:49:04 rms-change max change #iterations 4.784823 225.3469 at 10iterations 2.300185 90.54899 at 20iterations 1.109802 30.04329 at 30iterations 0.5350294 17.96132 at 40iterations 0.2582751 7.503277 at 50iterations 0.1247701 3.488756 at 60iterations 6.0197122E-02 1.633985 at 70iterations 2.8973116E-02 0.7873387 at 80iterations 1.3993770E-02 0.4018974 at 90iterations 6.7862440E-03 0.1799469 at 100iterations 3.2741411E-03 0.1001682 at 110iterations 1.5910569E-03 4.8952103E-02 at 120iterations finished qdiffx linear iterations at : 03:49:10 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 1.5910569E-03 4.8952103E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 03:49:11 7.150u 0.170s 0:07.64 95.8% 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 03:49:11 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: 350 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2833 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 !!! WARNING: TYS 1 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: 2.936432 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): -10.96700 36.50500 ymin,ymax (A): -27.01700 21.72400 zmin,zma (A): -9.001000 45.55500 x,y,z range (A): 47.47200 48.74100 54.55600 scale (grids/A): 2.936432 object centre (A): 12.76900 -2.646501 18.27700 number of atom coordinates read : 2833 total number of charged atoms : 2667 net assigned charge : 0.1130212 assigned positive charge : 429.6897 centred at (gu) : 89.43934 92.71684 96.09125 assigned negative charge : -429.5771 centred at (gu) : 88.22224 92.17395 95.78101 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 199569 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24492 grid for indexing accessible points = 1.400000 m= 105371 mr = 146751 m= 40377 mr = 87596 m= 10299 mr = 33235 m= 1583 mr = 7934 m= 112 mr = 1131 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 8224 time to turn everything in is 1.590000 number of dielectric boundary points 80621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 21334 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) : 1.957622 object centre at (A) : 12.76900 -2.646501 18.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6560629 0.3017231 midg,1,midg; midg,igrid,midg -0.2177821 3.4795921E-02 1,midg,midg; igrid,midg,midg -9.6987672E-02 0.5331311 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 1.880000 now iterating at: 03:49:13 rms-change max change #iterations 11.05897 516.6483 at 10iterations 6.526154 153.1518 at 20iterations 3.849033 90.31734 at 30iterations 2.264516 38.42502 at 40iterations 1.327548 26.30651 at 50iterations 0.7757503 17.13269 at 60iterations 0.4543878 8.128205 at 70iterations 0.2646207 4.720885 at 80iterations 0.1545174 2.745659 at 90iterations 9.0135187E-02 1.556198 at 100iterations 5.2592196E-02 0.8723412 at 110iterations 3.0631863E-02 0.5174851 at 120iterations 1.7875595E-02 0.2921677 at 130iterations 1.0473709E-02 0.1872749 at 140iterations 6.1539775E-03 9.8140717E-02 at 150iterations 3.6420154E-03 7.0941925E-02 at 160iterations 2.1814134E-03 4.0336609E-02 at 170iterations 1.3358233E-03 2.9724121E-02 at 180iterations finished qdiffx linear iterations at : 03:49:23 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 1.3358233E-03 2.9724121E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.79000 DelPhi exited at 03:49:24 11.797u 0.206s 0:12.74 94.1% 0+0k 0+0io 0pf+0w