Tue Oct 11 03:40:30 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 03:40:30 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: ZN3 302 has a net charge of 1.4000 !!! 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: 0.6060296 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): -11.05700 37.19500 ymin,ymax (A): -27.15600 21.24700 zmin,zma (A): -13.27700 45.46600 x,y,z range (A): 48.25200 48.40300 58.74300 scale (grids/A): 0.6060296 object centre (A): 13.06900 -2.954500 16.09450 number of atom coordinates read : 3211 total number of charged atoms : 2793 net assigned charge : 1.362021 assigned positive charge : 448.9952 centred at (gu) : 89.87943 90.92690 92.24879 assigned negative charge : -447.6341 centred at (gu) : 89.64685 90.87471 92.14176 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7007 nv = 96 ne = 84 npr = 60659 no. pairs analyzed = 60659 no. exposed pairs = 3417 no. arc points = 23793 no. surface atoms = 1164 nbur = 2047 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3976 m= 0 mr = 27 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.3700000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2461 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8862 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9214640E-09 9.9096003E-09 midg,1,midg; midg,igrid,midg -1.6671324E-09 3.9356163E-09 1,midg,midg; igrid,midg,midg -1.1770103E-08 1.1649560E-08 gauss-seidel spectral radius is 0.9859272 estimated iterations to convergence 69 setup time was (sec) 0.6500000 now iterating at: 03:40:31 rms-change max change #iterations 0.1243493 18.58833 at 10iterations 1.0970561E-02 1.470125 at 20iterations 9.9877594E-04 0.1701908 at 30iterations 1.2068256E-04 2.0035744E-02 at 40iterations 2.7380280E-05 5.5828094E-03 at 50iterations finished qdiffx linear iterations at : 03:40:35 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 2.7380280E-05 5.5828094E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 03:40:36 4.532u 0.385s 0:05.68 86.4% 0+0k 0+0io 4pf+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 03:40:36 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: ZN3 302 has a net charge of 1.4000 !!! 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: 1.818089 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): -11.05700 37.19500 ymin,ymax (A): -27.15600 21.24700 zmin,zma (A): -13.27700 45.46600 x,y,z range (A): 48.25200 48.40300 58.74300 scale (grids/A): 1.818089 object centre (A): 13.06900 -2.954500 16.09450 number of atom coordinates read : 3211 total number of charged atoms : 2793 net assigned charge : 1.362021 assigned positive charge : 448.9952 centred at (gu) : 89.63722 92.77995 96.74577 assigned negative charge : -447.6341 centred at (gu) : 88.94012 92.62382 96.42496 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 76465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23793 grid for indexing accessible points = 1.400000 m= 27055 mr = 54064 m= 3657 mr = 20295 m= 172 mr = 2172 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2637 time to turn everything in is 0.7100000 number of dielectric boundary points 30781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 196 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 21779 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) : 0.6060296 object centre at (A) : 13.06900 -2.954500 16.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5081096E-02 3.1371224E-03 midg,1,midg; midg,igrid,midg 4.0353276E-03 1.5061621E-03 1,midg,midg; igrid,midg,midg -8.0457488E-03 3.8245447E-02 gauss-seidel spectral radius is 0.9985321 estimated iterations to convergence 207 setup time was (sec) 1.050000 now iterating at: 03:40:37 rms-change max change #iterations 4.230124 198.9090 at 10iterations 1.929023 79.75160 at 20iterations 0.8795245 26.94361 at 30iterations 0.4007505 13.16317 at 40iterations 0.1827907 5.808578 at 50iterations 8.3365023E-02 2.613092 at 60iterations 3.8192779E-02 1.128538 at 70iterations 1.7431293E-02 0.5371857 at 80iterations 7.9759415E-03 0.2500210 at 90iterations 3.6479393E-03 0.1209602 at 100iterations 1.6789092E-03 5.4298401E-02 at 110iterations 7.7351963E-04 2.2964478E-02 at 120iterations finished qdiffx linear iterations at : 03:40:47 total time elapsed so far: 10.64000 # loops : 120 mean,max change (kT/e) : 7.7351963E-04 2.2964478E-02 energy calculations done at 10.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.81000 DelPhi exited at 03:40:48 10.814u 0.445s 0:12.21 92.1% 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 03:40:48 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIZ 79 has a net charge of 0.2000 !!! WARNING: HIZ 152 has a net charge of 0.2000 !!! WARNING: ZN3 301 has a net charge of 1.4000 !!! WARNING: ZN3 302 has a net charge of 1.4000 !!! 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: 2.727133 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): -11.05700 37.19500 ymin,ymax (A): -27.15600 21.24700 zmin,zma (A): -13.27700 45.46600 x,y,z range (A): 48.25200 48.40300 58.74300 scale (grids/A): 2.727133 object centre (A): 13.06900 -2.954500 16.09450 number of atom coordinates read : 3211 total number of charged atoms : 2793 net assigned charge : 1.362021 assigned positive charge : 448.9952 centred at (gu) : 89.45564 94.16985 100.1182 assigned negative charge : -447.6341 centred at (gu) : 88.41019 93.93562 99.63732 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 176962 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23793 grid for indexing accessible points = 1.400000 m= 89469 mr = 131070 m= 30625 mr = 73996 m= 6285 mr = 24667 m= 751 mr = 4570 m= 39 mr = 452 m= 0 mr = 12 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 8733 time to turn everything in is 1.610000 number of dielectric boundary points 69364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 22340 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) : 1.818089 object centre at (A) : 13.06900 -2.954500 16.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.078831 0.2372657 midg,1,midg; midg,igrid,midg 4.2754699E-02 -5.8666971E-02 1,midg,midg; igrid,midg,midg -6.6539191E-02 0.3741496 gauss-seidel spectral radius is 0.9992295 estimated iterations to convergence 284 setup time was (sec) 1.950000 now iterating at: 03:40:51 rms-change max change #iterations 10.00734 351.6605 at 10iterations 5.768406 135.2576 at 20iterations 3.305811 74.56271 at 30iterations 1.897934 45.94487 at 40iterations 1.083586 22.97654 at 50iterations 0.6187099 13.45840 at 60iterations 0.3522884 7.331120 at 70iterations 0.2015132 3.618279 at 80iterations 0.1147253 2.362867 at 90iterations 6.5240920E-02 1.291204 at 100iterations 3.7289105E-02 0.6935549 at 110iterations 2.1196589E-02 0.3883476 at 120iterations 1.2072087E-02 0.2137184 at 130iterations 6.8908609E-03 0.1239629 at 140iterations 3.9362786E-03 7.6116562E-02 at 150iterations 2.2607336E-03 4.1495323E-02 at 160iterations 1.3029294E-03 2.4144173E-02 at 170iterations 7.5792969E-04 1.5004158E-02 at 180iterations finished qdiffx linear iterations at : 03:41:07 total time elapsed so far: 18.06000 # loops : 180 mean,max change (kT/e) : 7.5792969E-04 1.5004158E-02 energy calculations done at 18.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.23000 DelPhi exited at 03:41:07 18.237u 0.490s 0:19.24 97.2% 0+0k 0+0io 0pf+0w