Wed Dec 21 14:21:27 PST 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 Wed Dec 21 2011 at 14:21:28 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6429939 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): -5.395000 33.95400 ymin,ymax (A): -3.505000 47.89900 zmin,zma (A): -7.990000 47.37600 x,y,z range (A): 39.34900 51.40400 55.36600 scale (grids/A): 0.6429939 object centre (A): 14.27950 22.19700 19.69300 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681008 assigned positive charge : 286.9501 centred at (gu) : 89.65442 92.60365 89.86624 assigned negative charge : -282.2693 centred at (gu) : 89.56081 92.73969 89.93700 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 40274 no. pairs analyzed = 40274 no. exposed pairs = 2480 no. arc points = 17141 no. surface atoms = 837 nbur = 1122 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 272 mr = 3073 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.2600000 number of dielectric boundary points 2699 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4582773E-08 1.2421697E-09 midg,1,midg; midg,igrid,midg 1.1590485E-08 -8.9968273E-09 1,midg,midg; igrid,midg,midg -9.5474628E-10 1.5080644E-08 gauss-seidel spectral radius is 0.9874109 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 14:21:30 rms-change max change #iterations 0.1233320 21.99520 at 10iterations 1.2195452E-02 2.000340 at 20iterations 1.2154754E-03 0.1947880 at 30iterations 1.2083256E-04 1.7654419E-02 at 40iterations 1.1918130E-05 1.8262863E-03 at 50iterations finished qdiffx linear iterations at : 14:21:33 total time elapsed so far: 4.180000 # loops : 50 mean,max change (kT/e) : 1.1918130E-05 1.8262863E-03 energy calculations done at 4.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 14:21:37 4.375u 0.401s 0:09.03 52.8% 0+0k 0+0io 6pf+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 Wed Dec 21 2011 at 14:21:38 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.928982 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): -5.395000 33.95400 ymin,ymax (A): -3.505000 47.89900 zmin,zma (A): -7.990000 47.37600 x,y,z range (A): 39.34900 51.40400 55.36600 scale (grids/A): 1.928982 object centre (A): 14.27950 22.19700 19.69300 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681008 assigned positive charge : 286.9501 centred at (gu) : 88.96330 97.81097 89.59884 assigned negative charge : -282.2693 centred at (gu) : 88.68272 98.21907 89.81111 start vw surface at 0.1100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59810 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17141 grid for indexing accessible points = 1.400000 m= 21299 mr = 41363 m= 3006 mr = 16103 m= 141 mr = 1913 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 2320 time to turn everything in is 0.6000000 number of dielectric boundary points 24821 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 14394 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) : 0.6429939 object centre at (A) : 14.27950 22.19700 19.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3844684E-02 3.6985181E-02 midg,1,midg; midg,igrid,midg 3.3745985E-02 -8.3797229E-03 1,midg,midg; igrid,midg,midg 7.5770910E-03 7.5516226E-03 gauss-seidel spectral radius is 0.9985901 estimated iterations to convergence 211 setup time was (sec) 1.120000 now iterating at: 14:21:40 rms-change max change #iterations 3.650613 177.2386 at 10iterations 1.691817 59.37959 at 20iterations 0.7863218 25.97114 at 30iterations 0.3625978 12.53562 at 40iterations 0.1671824 5.906132 at 50iterations 7.7160031E-02 2.517605 at 60iterations 3.5569597E-02 1.234016 at 70iterations 1.6477538E-02 0.6104145 at 80iterations 7.6110880E-03 0.2675295 at 90iterations 3.5298017E-03 0.1348991 at 100iterations 1.6344826E-03 5.3032875E-02 at 110iterations 7.5556594E-04 2.4829865E-02 at 120iterations finished qdiffx linear iterations at : 14:21:53 total time elapsed so far: 13.66000 # loops : 120 mean,max change (kT/e) : 7.5556594E-04 2.4829865E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.84000 DelPhi exited at 14:21:59 13.843u 0.825s 0:21.10 69.4% 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 Wed Dec 21 2011 at 14:22:00 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: 239 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1959 !!! WARNING: ASH 125 has a net charge of -0.3190 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.893472 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): -5.395000 33.95400 ymin,ymax (A): -3.505000 47.89900 zmin,zma (A): -7.990000 47.37600 x,y,z range (A): 39.34900 51.40400 55.36600 scale (grids/A): 2.893472 object centre (A): 14.27950 22.19700 19.69300 number of atom coordinates read : 1959 total number of charged atoms : 1826 net assigned charge : 4.681008 assigned positive charge : 286.9501 centred at (gu) : 88.44491 101.7165 89.39829 assigned negative charge : -282.2693 centred at (gu) : 88.02412 102.3287 89.71674 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 138177 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17141 grid for indexing accessible points = 1.400000 m= 69915 mr = 100093 m= 24550 mr = 57954 m= 5309 mr = 20241 m= 660 mr = 4018 m= 23 mr = 488 m= 0 mr = 6 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 8109 time to turn everything in is 1.430000 number of dielectric boundary points 55834 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 14606 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) : 1.928982 object centre at (A) : 14.27950 22.19700 19.69300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6802619E-03 0.9464046 midg,1,midg; midg,igrid,midg 0.3816865 -0.1284790 1,midg,midg; igrid,midg,midg 0.1398157 3.7245966E-02 gauss-seidel spectral radius is 0.9992336 estimated iterations to convergence 285 setup time was (sec) 1.780000 now iterating at: 14:22:04 rms-change max change #iterations 8.577120 388.4422 at 10iterations 4.939135 121.4219 at 20iterations 2.822108 81.69783 at 30iterations 1.607358 41.07304 at 40iterations 0.9162163 21.88797 at 50iterations 0.5220762 11.52449 at 60iterations 0.2964644 5.911911 at 70iterations 0.1685271 3.643260 at 80iterations 9.5825195E-02 1.876503 at 90iterations 5.4420706E-02 1.076412 at 100iterations 3.0895675E-02 0.5979290 at 110iterations 1.7574184E-02 0.3765926 at 120iterations 9.9741854E-03 0.2032318 at 130iterations 5.6618317E-03 0.1186190 at 140iterations 3.2144431E-03 6.7481995E-02 at 150iterations 1.8281365E-03 3.5008430E-02 at 160iterations 1.0371909E-03 2.2277832E-02 at 170iterations 5.8981101E-04 1.1415482E-02 at 180iterations finished qdiffx linear iterations at : 14:22:30 total time elapsed so far: 27.94000 # loops : 180 mean,max change (kT/e) : 5.8981101E-04 1.1415482E-02 energy calculations done at 27.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 28.11000 DelPhi exited at 14:22:35 28.119u 0.831s 0:35.62 81.2% 0+0k 0+0io 0pf+0w