Sun Oct 9 12:26:34 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 Sun Oct 9 2011 at 12:26:34 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 0.6891478 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): -14.22100 37.43700 ymin,ymax (A): -0.3520000 44.83800 zmin,zma (A): -7.024000 44.25400 x,y,z range (A): 51.65800 45.19000 51.27800 scale (grids/A): 0.6891478 object centre (A): 11.60800 22.24300 18.61500 number of atom coordinates read : 2433 total number of charged atoms : 2283 net assigned charge : 4.312022 assigned positive charge : 374.2131 centred at (gu) : 91.03619 91.27950 90.01583 assigned negative charge : -369.9016 centred at (gu) : 91.19807 91.37703 89.96873 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7711 nv = 96 ne = 84 npr = 48697 no. pairs analyzed = 48697 no. exposed pairs = 3088 no. arc points = 21462 no. surface atoms = 1034 nbur = 1399 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 492 mr = 4223 m= 0 mr = 70 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2023 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8769 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4207875E-09 4.2779540E-08 midg,1,midg; midg,igrid,midg 4.7908195E-08 -1.7700806E-08 1,midg,midg; igrid,midg,midg 6.9788207E-08 -4.8197354E-08 gauss-seidel spectral radius is 0.9890647 estimated iterations to convergence 78 setup time was (sec) 0.5500000 now iterating at: 12:26:35 rms-change max change #iterations 0.1979960 27.59819 at 10iterations 2.3321956E-02 3.205399 at 20iterations 3.2169947E-03 0.5688248 at 30iterations 6.7035813E-04 0.1033173 at 40iterations 2.0922933E-04 3.2047272E-02 at 50iterations finished qdiffx linear iterations at : 12:26:38 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.0922933E-04 3.2047272E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 12:26:38 3.465u 0.208s 0:04.04 90.5% 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 12:26:38 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.067444 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): -14.22100 37.43700 ymin,ymax (A): -0.3520000 44.83800 zmin,zma (A): -7.024000 44.25400 x,y,z range (A): 51.65800 45.19000 51.27800 scale (grids/A): 2.067444 object centre (A): 11.60800 22.24300 18.61500 number of atom coordinates read : 2433 total number of charged atoms : 2283 net assigned charge : 4.312022 assigned positive charge : 374.2131 centred at (gu) : 93.10818 93.83833 90.04689 assigned negative charge : -369.9016 centred at (gu) : 93.59409 94.13082 89.90598 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21462 grid for indexing accessible points = 1.400000 m= 31851 mr = 56470 m= 5995 mr = 23718 m= 549 mr = 3940 m= 10 mr = 246 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 0.6200000 number of dielectric boundary points 35735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 18086 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) : 0.6891478 object centre at (A) : 11.60800 22.24300 18.61500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5399741E-02 1.0259238E-02 midg,1,midg; midg,igrid,midg 4.2195652E-02 4.3820017E-03 1,midg,midg; igrid,midg,midg 2.0241946E-02 -4.4623904E-02 gauss-seidel spectral radius is 0.9988172 estimated iterations to convergence 230 setup time was (sec) 0.9200000 now iterating at: 12:26:39 rms-change max change #iterations 4.920224 231.5732 at 10iterations 2.412259 79.91174 at 20iterations 1.194457 35.58626 at 30iterations 0.5900255 18.68820 at 40iterations 0.2911047 8.486984 at 50iterations 0.1441377 4.216564 at 60iterations 7.1758606E-02 2.370807 at 70iterations 3.5304043E-02 1.116735 at 80iterations 1.7553255E-02 0.4808617 at 90iterations 8.8488134E-03 0.2718258 at 100iterations 4.5239748E-03 0.1289558 at 110iterations 2.3924846E-03 7.4915886E-02 at 120iterations finished qdiffx linear iterations at : 12:26:46 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.3924846E-03 7.4915886E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 12:26:47 7.982u 0.254s 0:08.50 96.8% 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 12:26:47 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2433 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 3.101165 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): -14.22100 37.43700 ymin,ymax (A): -0.3520000 44.83800 zmin,zma (A): -7.024000 44.25400 x,y,z range (A): 51.65800 45.19000 51.27800 scale (grids/A): 3.101165 object centre (A): 11.60800 22.24300 18.61500 number of atom coordinates read : 2433 total number of charged atoms : 2283 net assigned charge : 4.312022 assigned positive charge : 374.2131 centred at (gu) : 94.66216 95.75749 90.07024 assigned negative charge : -369.9016 centred at (gu) : 95.39114 96.19629 89.85899 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 188241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21462 grid for indexing accessible points = 1.400000 m= 99819 mr = 136565 m= 39933 mr = 81821 m= 11291 mr = 32444 m= 2168 mr = 8569 m= 228 mr = 1561 m= 6 mr = 132 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 80593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 18264 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) : 2.067444 object centre at (A) : 11.60800 22.24300 18.61500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2384870 -0.1704212 midg,1,midg; midg,igrid,midg 0.3621357 -6.6745080E-02 1,midg,midg; igrid,midg,midg 0.3700985 -0.5100104 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 2.210000 now iterating at: 12:26:49 rms-change max change #iterations 11.12691 511.3967 at 10iterations 6.610542 150.4548 at 20iterations 3.905845 76.66836 at 30iterations 2.302991 41.48612 at 40iterations 1.359091 24.73258 at 50iterations 0.7976698 13.75247 at 60iterations 0.4683022 8.608915 at 70iterations 0.2738497 4.534988 at 80iterations 0.1607880 3.263826 at 90iterations 9.4190963E-02 1.487785 at 100iterations 5.5483025E-02 0.9964676 at 110iterations 3.2647010E-02 0.5730095 at 120iterations 1.9394943E-02 0.3536062 at 130iterations 1.1706918E-02 0.2277298 at 140iterations 7.2446303E-03 0.1370945 at 150iterations 4.7065662E-03 9.6977234E-02 at 160iterations 3.2237726E-03 7.2723389E-02 at 170iterations 2.3558377E-03 5.2429199E-02 at 180iterations finished qdiffx linear iterations at : 12:27:00 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 2.3558377E-03 5.2429199E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.55000 DelPhi exited at 12:27:01 13.552u 0.300s 0:14.13 98.0% 0+0k 0+0io 0pf+0w