Sat Oct 8 16:05:39 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 Sat Oct 8 2011 at 16:05:39 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6537628 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): -2.001000 45.77700 ymin,ymax (A): -16.58900 29.21400 zmin,zma (A): -17.77800 36.67600 x,y,z range (A): 47.77800 45.80300 54.45400 scale (grids/A): 0.6537628 object centre (A): 21.88800 6.312499 9.448999 number of atom coordinates read : 2300 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 344.2781 centred at (gu) : 90.58358 88.88979 90.22234 assigned negative charge : -340.3788 centred at (gu) : 90.63664 89.03313 90.27583 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6664 nv = 96 ne = 84 npr = 46214 no. pairs analyzed = 46214 no. exposed pairs = 2969 no. arc points = 20289 no. surface atoms = 1001 nbur = 1299 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3665 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.3100000 number of dielectric boundary points 3338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1956 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7966 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5302568E-08 2.2915915E-10 midg,1,midg; midg,igrid,midg 3.6707274E-08 -1.0409413E-08 1,midg,midg; igrid,midg,midg 1.4143872E-08 2.8004363E-10 gauss-seidel spectral radius is 0.9878507 estimated iterations to convergence 74 setup time was (sec) 0.5900000 now iterating at: 16:05:40 rms-change max change #iterations 0.1516698 22.44167 at 10iterations 1.5612951E-02 2.402084 at 20iterations 1.6724422E-03 0.2653770 at 30iterations 1.8726673E-04 2.9232025E-02 at 40iterations 2.7356524E-05 4.2219162E-03 at 50iterations finished qdiffx linear iterations at : 16:05:43 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.7356524E-05 4.2219162E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 16:05:43 4.108u 0.275s 0:04.69 93.1% 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 Sat Oct 8 2011 at 16:05:43 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.961288 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): -2.001000 45.77700 ymin,ymax (A): -16.58900 29.21400 zmin,zma (A): -17.77800 36.67600 x,y,z range (A): 47.77800 45.80300 54.45400 scale (grids/A): 1.961288 object centre (A): 21.88800 6.312499 9.448999 number of atom coordinates read : 2300 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 344.2781 centred at (gu) : 91.75030 86.66913 90.66652 assigned negative charge : -340.3788 centred at (gu) : 91.90988 87.09944 90.82730 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 71475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20289 grid for indexing accessible points = 1.400000 m= 26632 mr = 49382 m= 4853 mr = 19795 m= 328 mr = 3303 m= 7 mr = 144 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 0.6500000 number of dielectric boundary points 30671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17582 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) : 0.6537628 object centre at (A) : 21.88800 6.312499 9.448999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4584319E-02 -1.7175993E-02 midg,1,midg; midg,igrid,midg 3.1119520E-02 -5.8463546E-03 1,midg,midg; igrid,midg,midg 5.7302848E-03 -3.8502645E-02 gauss-seidel spectral radius is 0.9986836 estimated iterations to convergence 218 setup time was (sec) 0.9500000 now iterating at: 16:05:45 rms-change max change #iterations 4.221130 182.6317 at 10iterations 2.003711 67.85419 at 20iterations 0.9502520 33.07869 at 30iterations 0.4540013 16.50161 at 40iterations 0.2149397 6.563118 at 50iterations 0.1024458 3.517172 at 60iterations 4.8621196E-02 1.570356 at 70iterations 2.3099160E-02 0.7405248 at 80iterations 1.0996399E-02 0.3500724 at 90iterations 5.2493056E-03 0.1686478 at 100iterations 2.4942397E-03 7.8205109E-02 at 110iterations 1.1883425E-03 3.7750244E-02 at 120iterations finished qdiffx linear iterations at : 16:05:53 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 1.1883425E-03 3.7750244E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 16:05:54 9.576u 0.308s 0:10.17 97.0% 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 Sat Oct 8 2011 at 16:05:54 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: ASL 705 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.941933 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): -2.001000 45.77700 ymin,ymax (A): -16.58900 29.21400 zmin,zma (A): -17.77800 36.67600 x,y,z range (A): 47.77800 45.80300 54.45400 scale (grids/A): 2.941933 object centre (A): 21.88800 6.312499 9.448999 number of atom coordinates read : 2300 total number of charged atoms : 2230 net assigned charge : 3.900002 assigned positive charge : 344.2781 centred at (gu) : 92.62527 85.00352 90.99972 assigned negative charge : -340.3788 centred at (gu) : 92.86474 85.64915 91.24098 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 165285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20289 grid for indexing accessible points = 1.400000 m= 84173 mr = 119819 m= 32733 mr = 68928 m= 9104 mr = 26720 m= 1466 mr = 7196 m= 120 mr = 1059 m= 5 mr = 57 m= 0 mr = 2 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 3192 time to turn everything in is 1.680000 number of dielectric boundary points 69105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 17839 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) : 1.961288 object centre at (A) : 21.88800 6.312499 9.448999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2380355 -0.2457793 midg,1,midg; midg,igrid,midg 0.2568669 -8.0919757E-02 1,midg,midg; igrid,midg,midg 4.6966627E-02 -0.5376014 gauss-seidel spectral radius is 0.9992712 estimated iterations to convergence 292 setup time was (sec) 2.010000 now iterating at: 16:05:56 rms-change max change #iterations 9.762244 428.4944 at 10iterations 5.704335 122.7666 at 20iterations 3.331447 80.42941 at 30iterations 1.944699 42.48516 at 40iterations 1.132243 20.64812 at 50iterations 0.6600485 13.16767 at 60iterations 0.3818346 7.693931 at 70iterations 0.2212435 4.026993 at 80iterations 0.1282803 2.433881 at 90iterations 7.4240081E-02 1.415955 at 100iterations 4.3069489E-02 0.7650584 at 110iterations 2.4819611E-02 0.4885112 at 120iterations 1.4353151E-02 0.2697906 at 130iterations 8.3025470E-03 0.1681042 at 140iterations 4.7885543E-03 8.6179733E-02 at 150iterations 2.7720039E-03 4.7108650E-02 at 160iterations 1.5986157E-03 3.0689240E-02 at 170iterations 9.2522003E-04 1.5708923E-02 at 180iterations finished qdiffx linear iterations at : 16:06:10 total time elapsed so far: 16.15000 # loops : 180 mean,max change (kT/e) : 9.2522003E-04 1.5708923E-02 energy calculations done at 16.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.34000 DelPhi exited at 16:06:11 16.338u 0.317s 0:17.01 97.8% 0+0k 0+0io 0pf+0w