Thu Jan 19 13:33:54 PST 2012 #!/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 Thu Jan 19 2012 at 13:33:54 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: 375 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7773 !!! WARNING: LYS 51 has a net charge of 0.0730 !!! WARNING: LYS 65 has a net charge of 0.1210 !!! WARNING: LYS 138 has a net charge of 0.0730 !!! WARNING: GLU 139 has a net charge of -0.2080 !!! WARNING: LYS 144 has a net charge of 0.1210 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: ARG 191 has a net charge of 0.2090 !!! WARNING: LYS 327 has a net charge of 0.1210 !!! WARNING: LYS 374 has a net charge of 0.0730 !!! WARNING: LYS 442 has a net charge of 0.0730 !!! WARNING: LYS 480 has a net charge of 0.3390 !!! WARNING: SEP 499 has a net charge of -0.2750 !!! WARNING: LYS 598 has a net charge of 0.1210 !!! WARNING: LYS 634 has a net charge of 0.3390 !!! WARNING: ASP 759 has a net charge of 0.4120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4319759 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): -3.211000 75.40500 ymin,ymax (A): -11.13000 57.69400 zmin,zma (A): -7.855000 74.55700 x,y,z range (A): 78.61600 68.82400 82.41200 scale (grids/A): 0.4319759 object centre (A): 36.09700 23.28200 33.35100 number of atom coordinates read : 7773 total number of charged atoms : 7492 net assigned charge : -3.387948 assigned positive charge : 1174.966 centred at (gu) : 89.55403 89.81165 89.74394 assigned negative charge : -1178.363 centred at (gu) : 89.52689 89.83380 89.61118 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8570 nv = 96 ne = 84 npr = 156582 no. pairs analyzed = 156582 no. exposed pairs = 9823 no. arc points = 66535 no. surface atoms = 3308 nbur = 4465 mkacc time = 0.2700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.932000 m= 240 mr = 4196 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5450 ## 1125 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11707 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2636663E-11 9.0159573E-12 midg,1,midg; midg,igrid,midg 1.1192922E-12 -2.3787933E-12 1,midg,midg; igrid,midg,midg -3.3607197E-12 1.2613148E-12 gauss-seidel spectral radius is 0.9728630 estimated iterations to convergence 51 setup time was (sec) 0.6900000 now iterating at: 13:33:58 rms-change max change #iterations 3.4327064E-02 5.056743 at 10iterations 1.7197975E-03 0.2834778 at 20iterations 5.1720231E-04 6.3942909E-02 at 30iterations 2.1819164E-04 2.7150631E-02 at 40iterations 9.2859031E-05 1.1669636E-02 at 50iterations finished qdiffx linear iterations at : 13:34:06 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 9.2859031E-05 1.1669636E-02 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 13:34:08 3.882u 0.182s 0:14.14 28.7% 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 Thu Jan 19 2012 at 13:34:09 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: 375 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7773 !!! WARNING: LYS 51 has a net charge of 0.0730 !!! WARNING: LYS 65 has a net charge of 0.1210 !!! WARNING: LYS 138 has a net charge of 0.0730 !!! WARNING: GLU 139 has a net charge of -0.2080 !!! WARNING: LYS 144 has a net charge of 0.1210 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: ARG 191 has a net charge of 0.2090 !!! WARNING: LYS 327 has a net charge of 0.1210 !!! WARNING: LYS 374 has a net charge of 0.0730 !!! WARNING: LYS 442 has a net charge of 0.0730 !!! WARNING: LYS 480 has a net charge of 0.3390 !!! WARNING: SEP 499 has a net charge of -0.2750 !!! WARNING: LYS 598 has a net charge of 0.1210 !!! WARNING: LYS 634 has a net charge of 0.3390 !!! WARNING: ASP 759 has a net charge of 0.4120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.295928 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): -3.211000 75.40500 ymin,ymax (A): -11.13000 57.69400 zmin,zma (A): -7.855000 74.55700 x,y,z range (A): 78.61600 68.82400 82.41200 scale (grids/A): 1.295928 object centre (A): 36.09700 23.28200 33.35100 number of atom coordinates read : 7773 total number of charged atoms : 7492 net assigned charge : -3.387948 assigned positive charge : 1174.966 centred at (gu) : 88.66134 89.43364 89.23051 assigned negative charge : -1178.363 centred at (gu) : 88.58118 89.50125 88.83349 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 102373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 66535 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 23173 mr = 69500 m= 1097 mr = 13488 m= 7 mr = 231 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 252 time to turn everything in is 0.5300000 number of dielectric boundary points 43431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1191 ## 39 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 52092 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) : 0.4319759 object centre at (A) : 36.09700 23.28200 33.35100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7045444E-02 4.5075589E-03 midg,1,midg; midg,igrid,midg 1.0783773E-04 -3.3434764E-03 1,midg,midg; igrid,midg,midg -2.3585034E-03 4.8113363E-03 gauss-seidel spectral radius is 0.9975187 estimated iterations to convergence 160 setup time was (sec) 0.7600000 now iterating at: 13:34:10 rms-change max change #iterations 3.378656 117.7921 at 10iterations 1.214934 39.64845 at 20iterations 0.4381158 13.78537 at 30iterations 0.1585549 4.913367 at 40iterations 5.7207815E-02 1.794101 at 50iterations 2.0807039E-02 0.7256308 at 60iterations 7.5714518E-03 0.2295742 at 70iterations 2.8144368E-03 9.5443726E-02 at 80iterations 1.1185255E-03 4.1802298E-02 at 90iterations 5.2251387E-04 1.7574310E-02 at 100iterations 3.0514726E-04 9.4895363E-03 at 110iterations 2.0486736E-04 5.4092407E-03 at 120iterations finished qdiffx linear iterations at : 13:34:32 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 2.0486736E-04 5.4092407E-03 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.320000 DelPhi exited at 13:34:33 8.322u 0.218s 0:24.26 35.1% 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 Thu Jan 19 2012 at 13:34:33 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: 375 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 7773 !!! WARNING: LYS 51 has a net charge of 0.0730 !!! WARNING: LYS 65 has a net charge of 0.1210 !!! WARNING: LYS 138 has a net charge of 0.0730 !!! WARNING: GLU 139 has a net charge of -0.2080 !!! WARNING: LYS 144 has a net charge of 0.1210 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: ARG 191 has a net charge of 0.2090 !!! WARNING: LYS 327 has a net charge of 0.1210 !!! WARNING: LYS 374 has a net charge of 0.0730 !!! WARNING: LYS 442 has a net charge of 0.0730 !!! WARNING: LYS 480 has a net charge of 0.3390 !!! WARNING: SEP 499 has a net charge of -0.2750 !!! WARNING: LYS 598 has a net charge of 0.1210 !!! WARNING: LYS 634 has a net charge of 0.3390 !!! WARNING: ASP 759 has a net charge of 0.4120 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.943892 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): -3.211000 75.40500 ymin,ymax (A): -11.13000 57.69400 zmin,zma (A): -7.855000 74.55700 x,y,z range (A): 78.61600 68.82400 82.41200 scale (grids/A): 1.943892 object centre (A): 36.09700 23.28200 33.35100 number of atom coordinates read : 7773 total number of charged atoms : 7492 net assigned charge : -3.387948 assigned positive charge : 1174.966 centred at (gu) : 87.99188 89.15015 88.84531 assigned negative charge : -1178.363 centred at (gu) : 87.87183 89.25183 88.25022 start vw surface at 0.1900000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 240940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 66535 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 91501 mr = 173417 m= 15278 mr = 67566 m= 1129 mr = 9288 m= 17 mr = 444 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 912 time to turn everything in is 1.320000 number of dielectric boundary points 98150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 59129 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) : 1.295928 object centre at (A) : 36.09700 23.28200 33.35100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4879237 8.5660122E-02 midg,1,midg; midg,igrid,midg 1.1466400E-02 -9.0659894E-02 1,midg,midg; igrid,midg,midg -0.1542055 0.1869168 gauss-seidel spectral radius is 0.9990410 estimated iterations to convergence 255 setup time was (sec) 1.640000 now iterating at: 13:34:41 rms-change max change #iterations 10.39254 421.2578 at 10iterations 5.790148 174.5751 at 20iterations 3.188540 79.39082 at 30iterations 1.738119 38.73420 at 40iterations 0.9457159 21.22927 at 50iterations 0.5131772 13.47568 at 60iterations 0.2768179 6.653700 at 70iterations 0.1488522 3.169984 at 80iterations 8.0066018E-02 1.773354 at 90iterations 4.2991880E-02 0.8676546 at 100iterations 2.3001615E-02 0.4837990 at 110iterations 1.2334085E-02 0.2549706 at 120iterations 6.5934695E-03 0.1343098 at 130iterations 3.5254417E-03 6.7863464E-02 at 140iterations 1.8897313E-03 3.8799286E-02 at 150iterations 1.0143095E-03 2.0303726E-02 at 160iterations 5.4740341E-04 1.0181427E-02 at 170iterations 2.9921348E-04 5.8002472E-03 at 180iterations finished qdiffx linear iterations at : 13:35:15 total time elapsed so far: 15.20000 # loops : 180 mean,max change (kT/e) : 2.9921348E-04 5.8002472E-03 energy calculations done at 15.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.34000 DelPhi exited at 13:35:16 15.346u 0.305s 0:42.49 36.8% 0+0k 0+0io 0pf+0w