Tue Oct 11 03:43:06 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 Tue Oct 11 2011 at 03:43:06 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6591128 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): -11.63700 36.94700 ymin,ymax (A): -27.12800 21.48200 zmin,zma (A): -8.409000 45.60300 x,y,z range (A): 48.58400 48.61000 54.01200 scale (grids/A): 0.6591128 object centre (A): 12.65500 -2.823000 18.59700 number of atom coordinates read : 3077 total number of charged atoms : 2673 net assigned charge : -0.8379811 assigned positive charge : 425.1316 centred at (gu) : 90.06950 90.71073 91.37411 assigned negative charge : -425.9703 centred at (gu) : 89.79745 90.65534 91.32012 start vw surface at 0.1300000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8273 nv = 96 ne = 84 npr = 57754 no. pairs analyzed = 57754 no. exposed pairs = 3341 no. arc points = 23437 no. surface atoms = 1116 nbur = 1961 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4829 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.3500000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0353069E-08 1.2231774E-08 midg,1,midg; midg,igrid,midg -1.2145280E-08 1.0925518E-08 1,midg,midg; igrid,midg,midg -6.0732631E-08 5.4507559E-08 gauss-seidel spectral radius is 0.9880874 estimated iterations to convergence 75 setup time was (sec) 0.6900000 now iterating at: 03:43:07 rms-change max change #iterations 0.1737745 22.01186 at 10iterations 1.9049702E-02 2.477521 at 20iterations 2.1110489E-03 0.2727509 at 30iterations 3.0449106E-04 3.5957336E-02 at 40iterations 6.9861679E-05 7.2469711E-03 at 50iterations finished qdiffx linear iterations at : 03:43:12 total time elapsed so far: 6.250000 # loops : 50 mean,max change (kT/e) : 6.9861679E-05 7.2469711E-03 energy calculations done at 6.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.410000 DelPhi exited at 03:43:13 6.410u 0.513s 0:07.42 93.2% 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 Tue Oct 11 2011 at 03:43:13 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.977338 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): -11.63700 36.94700 ymin,ymax (A): -27.12800 21.48200 zmin,zma (A): -8.409000 45.60300 x,y,z range (A): 48.58400 48.61000 54.01200 scale (grids/A): 1.977338 object centre (A): 12.65500 -2.823000 18.59700 number of atom coordinates read : 3077 total number of charged atoms : 2673 net assigned charge : -0.8379811 assigned positive charge : 425.1316 centred at (gu) : 90.20778 92.13176 94.12164 assigned negative charge : -425.9703 centred at (gu) : 89.39199 91.96584 93.95988 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23437 grid for indexing accessible points = 1.400000 m= 34585 mr = 63812 m= 5885 mr = 26465 m= 373 mr = 3798 m= 8 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 183 time to turn everything in is 0.8000000 number of dielectric boundary points 35519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21079 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) : 0.6591128 object centre at (A) : 12.65500 -2.823000 18.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8828552E-02 8.5230712E-03 midg,1,midg; midg,igrid,midg -1.0949460E-02 -4.2540566E-03 1,midg,midg; igrid,midg,midg -1.5563617E-02 6.8137489E-02 gauss-seidel spectral radius is 0.9987498 estimated iterations to convergence 224 setup time was (sec) 1.170000 now iterating at: 03:43:15 rms-change max change #iterations 4.818124 224.7716 at 10iterations 2.340360 84.20473 at 20iterations 1.134648 36.42303 at 30iterations 0.5509818 17.79042 at 40iterations 0.2683875 7.553261 at 50iterations 0.1297808 4.083338 at 60iterations 6.2920466E-02 1.819778 at 70iterations 3.0520070E-02 0.8360710 at 80iterations 1.4831870E-02 0.4105825 at 90iterations 7.2380169E-03 0.2038536 at 100iterations 3.5413480E-03 0.1060452 at 110iterations 1.7473631E-03 5.4282188E-02 at 120iterations finished qdiffx linear iterations at : 03:43:28 total time elapsed so far: 13.76000 # loops : 120 mean,max change (kT/e) : 1.7473631E-03 5.4282188E-02 energy calculations done at 13.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 03:43:29 13.942u 0.624s 0:15.98 91.1% 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 Tue Oct 11 2011 at 03:43:29 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3077 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.966007 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): -11.63700 36.94700 ymin,ymax (A): -27.12800 21.48200 zmin,zma (A): -8.409000 45.60300 x,y,z range (A): 48.58400 48.61000 54.01200 scale (grids/A): 2.966007 object centre (A): 12.65500 -2.823000 18.59700 number of atom coordinates read : 3077 total number of charged atoms : 2673 net assigned charge : -0.8379811 assigned positive charge : 425.1316 centred at (gu) : 90.31150 93.19759 96.18223 assigned negative charge : -425.9703 centred at (gu) : 89.08780 92.94872 95.93977 start vw surface at 0.1400000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 205348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23437 grid for indexing accessible points = 1.400000 m= 109985 mr = 153506 m= 42456 mr = 92320 m= 10784 mr = 35032 m= 1559 mr = 8147 m= 118 mr = 1022 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 671 time to turn everything in is 2.010000 number of dielectric boundary points 80156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 21373 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) : 1.977338 object centre at (A) : 12.65500 -2.823000 18.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1826402 0.2800154 midg,1,midg; midg,igrid,midg -0.1422754 4.6051528E-02 1,midg,midg; igrid,midg,midg -5.6939859E-02 0.6068679 gauss-seidel spectral radius is 0.9992846 estimated iterations to convergence 295 setup time was (sec) 2.470000 now iterating at: 03:43:34 rms-change max change #iterations 11.05545 425.2078 at 10iterations 6.511899 158.1571 at 20iterations 3.822024 83.10023 at 30iterations 2.242311 44.84824 at 40iterations 1.314092 23.37637 at 50iterations 0.7672626 14.79064 at 60iterations 0.4482863 8.544107 at 70iterations 0.2615600 4.506351 at 80iterations 0.1524708 2.812872 at 90iterations 8.8765815E-02 1.560301 at 100iterations 5.1715851E-02 0.8850250 at 110iterations 3.0150656E-02 0.6041756 at 120iterations 1.7541971E-02 0.2966919 at 130iterations 1.0211128E-02 0.1734619 at 140iterations 5.9696408E-03 9.7999573E-02 at 150iterations 3.4997179E-03 6.1946869E-02 at 160iterations 2.0587114E-03 3.4584045E-02 at 170iterations 1.2204398E-03 2.1093369E-02 at 180iterations finished qdiffx linear iterations at : 03:43:57 total time elapsed so far: 24.35000 # loops : 180 mean,max change (kT/e) : 1.2204398E-03 2.1093369E-02 energy calculations done at 24.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.51000 DelPhi exited at 03:43:59 24.517u 0.688s 0:29.58 85.1% 0+0k 0+0io 0pf+0w