Tue Oct 11 04:12:28 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 04:12:28 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! 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: 0.6434239 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): -9.511000 35.92300 ymin,ymax (A): -26.81300 21.67700 zmin,zma (A): -10.11000 45.21900 x,y,z range (A): 45.43400 48.49000 55.32900 scale (grids/A): 0.6434239 object centre (A): 13.20600 -2.568000 17.55450 number of atom coordinates read : 2762 total number of charged atoms : 2624 net assigned charge : 2.588016 assigned positive charge : 423.1397 centred at (gu) : 89.69946 90.52550 91.70879 assigned negative charge : -420.5522 centred at (gu) : 89.45956 90.37508 91.68359 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7539 nv = 96 ne = 84 npr = 55622 no. pairs analyzed = 55622 no. exposed pairs = 3440 no. arc points = 23526 no. surface atoms = 1157 nbur = 1605 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4200 m= 5 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3100000 number of dielectric boundary points 3689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2308 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 9208 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9487142E-10 1.0938737E-08 midg,1,midg; midg,igrid,midg -1.5157676E-08 2.7536119E-08 1,midg,midg; igrid,midg,midg -3.1960973E-08 3.4158351E-08 gauss-seidel spectral radius is 0.9874947 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 04:12:28 rms-change max change #iterations 0.1585510 28.00742 at 10iterations 1.6175183E-02 2.389874 at 20iterations 1.6409708E-03 0.2333741 at 30iterations 1.7100081E-04 2.5432587E-02 at 40iterations 1.9113324E-05 2.2048950E-03 at 50iterations finished qdiffx linear iterations at : 04:12:31 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.9113324E-05 2.2048950E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 04:12:31 3.118u 0.149s 0:03.66 88.7% 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 04:12:31 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.930272 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): -9.511000 35.92300 ymin,ymax (A): -26.81300 21.67700 zmin,zma (A): -10.11000 45.21900 x,y,z range (A): 45.43400 48.49000 55.32900 scale (grids/A): 1.930272 object centre (A): 13.20600 -2.568000 17.55450 number of atom coordinates read : 2762 total number of charged atoms : 2624 net assigned charge : 2.588016 assigned positive charge : 423.1397 centred at (gu) : 89.09754 91.57606 95.12561 assigned negative charge : -420.5522 centred at (gu) : 88.37830 91.12466 95.05049 start vw surface at 0.2500000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 81631 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23526 grid for indexing accessible points = 1.400000 m= 29867 mr = 57348 m= 4670 mr = 22067 m= 256 mr = 2869 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 376 time to turn everything in is 0.6600000 number of dielectric boundary points 34058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20672 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) : 0.6434239 object centre at (A) : 13.20600 -2.568000 17.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.3354673E-03 7.8197913E-03 midg,1,midg; midg,igrid,midg -1.9197762E-02 7.9505965E-03 1,midg,midg; igrid,midg,midg -1.6037207E-02 5.3716686E-02 gauss-seidel spectral radius is 0.9986848 estimated iterations to convergence 218 setup time was (sec) 0.9300000 now iterating at: 04:12:33 rms-change max change #iterations 4.590044 184.5316 at 10iterations 2.182567 72.48022 at 20iterations 1.040040 31.81414 at 30iterations 0.4942766 14.77705 at 40iterations 0.2352045 7.535704 at 50iterations 0.1120160 3.494822 at 60iterations 5.3271148E-02 1.747685 at 70iterations 2.5378417E-02 0.8526840 at 80iterations 1.2053449E-02 0.3591080 at 90iterations 5.7420116E-03 0.1814671 at 100iterations 2.7217425E-03 8.0997467E-02 at 110iterations 1.3001441E-03 3.9876461E-02 at 120iterations finished qdiffx linear iterations at : 04:12:39 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 1.3001441E-03 3.9876461E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 04:12:40 7.100u 0.166s 0:08.70 83.4% 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 Tue Oct 11 2011 at 04:12:40 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2762 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.895407 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): -9.511000 35.92300 ymin,ymax (A): -26.81300 21.67700 zmin,zma (A): -10.11000 45.21900 x,y,z range (A): 45.43400 48.49000 55.32900 scale (grids/A): 2.895407 object centre (A): 13.20600 -2.568000 17.55450 number of atom coordinates read : 2762 total number of charged atoms : 2624 net assigned charge : 2.588016 assigned positive charge : 423.1397 centred at (gu) : 88.64615 92.36383 97.68828 assigned negative charge : -420.5522 centred at (gu) : 87.56738 91.68703 97.57558 start vw surface at 0.2300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 188794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23526 grid for indexing accessible points = 1.400000 m= 96508 mr = 138873 m= 35147 mr = 79152 m= 8393 mr = 28148 m= 1098 mr = 6242 m= 53 mr = 682 m= 0 mr = 19 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1381 time to turn everything in is 1.500000 number of dielectric boundary points 76877 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 20970 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) : 1.930272 object centre at (A) : 13.20600 -2.568000 17.55450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2700959 0.2758600 midg,1,midg; midg,igrid,midg -0.1992013 2.2601129E-02 1,midg,midg; igrid,midg,midg -9.0411596E-02 0.4668751 gauss-seidel spectral radius is 0.9992703 estimated iterations to convergence 292 setup time was (sec) 1.790000 now iterating at: 04:12:42 rms-change max change #iterations 10.63273 365.1288 at 10iterations 6.230185 131.2034 at 20iterations 3.643847 66.98711 at 30iterations 2.123879 43.01743 at 40iterations 1.233107 21.95905 at 50iterations 0.7176993 12.83834 at 60iterations 0.4159762 7.819141 at 70iterations 0.2413077 4.360123 at 80iterations 0.1397188 2.739933 at 90iterations 8.0794670E-02 1.509854 at 100iterations 4.6770722E-02 0.9623566 at 110iterations 2.7059151E-02 0.4704247 at 120iterations 1.5635012E-02 0.3124847 at 130iterations 9.0718055E-03 0.1548491 at 140iterations 5.2534030E-03 9.7648621E-02 at 150iterations 3.0465482E-03 5.2814484E-02 at 160iterations 1.7788972E-03 3.0765533E-02 at 170iterations 1.0400675E-03 1.8131256E-02 at 180iterations finished qdiffx linear iterations at : 04:12:52 total time elapsed so far: 11.83000 # loops : 180 mean,max change (kT/e) : 1.0400675E-03 1.8131256E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 04:12:53 12.008u 0.180s 0:12.76 95.4% 0+0k 0+0io 0pf+0w