Sun Oct 9 12:21:12 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 Sun Oct 9 2011 at 12:21:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 0.6864901 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): -14.32300 37.35800 ymin,ymax (A): -1.185000 44.82800 zmin,zma (A): -8.213000 43.64500 x,y,z range (A): 51.68100 46.01300 51.85800 scale (grids/A): 0.6864901 object centre (A): 11.51750 21.82150 17.71600 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 369.1930 centred at (gu) : 90.92551 91.49241 90.46140 assigned negative charge : -365.6936 centred at (gu) : 91.11916 91.55680 90.44028 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7537 nv = 96 ne = 84 npr = 48411 no. pairs analyzed = 48411 no. exposed pairs = 3173 no. arc points = 21536 no. surface atoms = 1071 nbur = 1340 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 523 mr = 4125 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2017 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0347596E-08 2.8856935E-08 midg,1,midg; midg,igrid,midg 3.0978430E-08 -6.2862155E-09 1,midg,midg; igrid,midg,midg 7.1833355E-08 -6.2763753E-08 gauss-seidel spectral radius is 0.9889793 estimated iterations to convergence 78 setup time was (sec) 0.4900000 now iterating at: 12:21:12 rms-change max change #iterations 0.1859259 27.61728 at 10iterations 2.1530572E-02 2.868670 at 20iterations 2.5801181E-03 0.3429699 at 30iterations 3.2411699E-04 5.0979614E-02 at 40iterations 5.9696813E-05 8.8348389E-03 at 50iterations finished qdiffx linear iterations at : 12:21:15 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 5.9696813E-05 8.8348389E-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 12:21:15 3.116u 0.150s 0:03.54 92.0% 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 Sun Oct 9 2011 at 12:21:15 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 2.059470 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): -14.32300 37.35800 ymin,ymax (A): -1.185000 44.82800 zmin,zma (A): -8.213000 43.64500 x,y,z range (A): 51.68100 46.01300 51.85800 scale (grids/A): 2.059470 object centre (A): 11.51750 21.82150 17.71600 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 369.1930 centred at (gu) : 92.77612 94.47680 91.38370 assigned negative charge : -365.6936 centred at (gu) : 93.35738 94.67028 91.32065 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 79474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21536 grid for indexing accessible points = 1.400000 m= 31067 mr = 54226 m= 5853 mr = 22966 m= 482 mr = 3804 m= 13 mr = 216 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 35677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17984 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) : 0.6864901 object centre at (A) : 11.51750 21.82150 17.71600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4361345E-02 2.7346334E-03 midg,1,midg; midg,igrid,midg 2.9239900E-02 -1.1158998E-03 1,midg,midg; igrid,midg,midg 2.9552242E-02 -6.0282253E-02 gauss-seidel spectral radius is 0.9988077 estimated iterations to convergence 229 setup time was (sec) 0.8900000 now iterating at: 12:21:16 rms-change max change #iterations 4.803359 255.9267 at 10iterations 2.356013 83.66380 at 20iterations 1.161788 35.45974 at 30iterations 0.5707837 17.28441 at 40iterations 0.2811958 8.948241 at 50iterations 0.1383831 3.923916 at 60iterations 6.8082854E-02 2.004895 at 70iterations 3.3589698E-02 0.9921265 at 80iterations 1.6508106E-02 0.4641522 at 90iterations 8.1514809E-03 0.2620354 at 100iterations 4.0145051E-03 0.1140137 at 110iterations 1.9899919E-03 5.6732178E-02 at 120iterations finished qdiffx linear iterations at : 12:21:22 total time elapsed so far: 6.860000 # loops : 120 mean,max change (kT/e) : 1.9899919E-03 5.6732178E-02 energy calculations done at 6.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 12:21:23 7.043u 0.171s 0:07.50 96.1% 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 Sun Oct 9 2011 at 12:21:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2411 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: 3.089205 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): -14.32300 37.35800 ymin,ymax (A): -1.185000 44.82800 zmin,zma (A): -8.213000 43.64500 x,y,z range (A): 51.68100 46.01300 51.85800 scale (grids/A): 3.089205 object centre (A): 11.51750 21.82150 17.71600 number of atom coordinates read : 2411 total number of charged atoms : 2269 net assigned charge : 3.500024 assigned positive charge : 369.1930 centred at (gu) : 94.16409 96.71510 92.07539 assigned negative charge : -365.6936 centred at (gu) : 95.03603 97.00543 91.98090 start vw surface at 0.2000000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 183230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21536 grid for indexing accessible points = 1.400000 m= 96104 mr = 131158 m= 39111 mr = 78530 m= 10859 mr = 31663 m= 1964 mr = 8207 m= 255 mr = 1313 m= 10 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.8700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 80495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 18152 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) : 2.059470 object centre at (A) : 11.51750 21.82150 17.71600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4714832 -0.2719362 midg,1,midg; midg,igrid,midg 0.2669631 -0.1283508 1,midg,midg; igrid,midg,midg 0.5028092 -0.7365167 gauss-seidel spectral radius is 0.9992951 estimated iterations to convergence 297 setup time was (sec) 2.130000 now iterating at: 12:21:25 rms-change max change #iterations 10.90699 515.8558 at 10iterations 6.458393 145.3416 at 20iterations 3.822314 80.74376 at 30iterations 2.255389 45.22655 at 40iterations 1.327839 24.45598 at 50iterations 0.7817022 14.13551 at 60iterations 0.4577588 8.436911 at 70iterations 0.2682675 4.554911 at 80iterations 0.1569907 2.855682 at 90iterations 9.1813788E-02 1.637095 at 100iterations 5.3675901E-02 0.9956541 at 110iterations 3.1412270E-02 0.6021795 at 120iterations 1.8382862E-02 0.3322945 at 130iterations 1.0756554E-02 0.1842995 at 140iterations 6.3639330E-03 0.1204948 at 150iterations 3.7641479E-03 8.0036163E-02 at 160iterations 2.2628049E-03 4.4265747E-02 at 170iterations 1.3925366E-03 2.8231621E-02 at 180iterations finished qdiffx linear iterations at : 12:21:35 total time elapsed so far: 11.56000 # loops : 180 mean,max change (kT/e) : 1.3925366E-03 2.8231621E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 12:21:35 11.779u 0.160s 0:12.40 96.2% 0+0k 0+0io 0pf+0w