Tue Oct 11 06:38:48 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 Tue Oct 11 2011 at 06:38:48 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7091492 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): -20.17600 24.67300 ymin,ymax (A): -28.57100 11.16200 zmin,zma (A): -13.50300 36.69800 x,y,z range (A): 44.84900 39.73300 50.20100 scale (grids/A): 0.7091492 object centre (A): 2.248501 -8.704500 11.59750 number of atom coordinates read : 2040 total number of charged atoms : 1906 net assigned charge : 6.931010 assigned positive charge : 309.1391 centred at (gu) : 89.89490 90.55286 89.47025 assigned negative charge : -302.2082 centred at (gu) : 89.70901 90.53024 89.44271 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6931 nv = 96 ne = 84 npr = 41051 no. pairs analyzed = 41051 no. exposed pairs = 2465 no. arc points = 16711 no. surface atoms = 834 nbur = 1206 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 449 mr = 3990 m= 5 mr = 84 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 0.2700000 number of dielectric boundary points 3311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1611 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7714 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2217672E-08 6.7622167E-08 midg,1,midg; midg,igrid,midg 4.4982666E-08 8.0327297E-08 1,midg,midg; igrid,midg,midg -3.3901603E-08 1.4879659E-07 gauss-seidel spectral radius is 0.9896287 estimated iterations to convergence 80 setup time was (sec) 0.4800000 now iterating at: 06:38:49 rms-change max change #iterations 0.1997277 28.61658 at 10iterations 2.5343304E-02 3.144588 at 20iterations 3.3801035E-03 0.4428606 at 30iterations 5.2653818E-04 6.8778992E-02 at 40iterations 1.2070152E-04 1.5134811E-02 at 50iterations finished qdiffx linear iterations at : 06:38:51 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.2070152E-04 1.5134811E-02 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 06:38:52 3.073u 0.175s 0:03.57 90.7% 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 Tue Oct 11 2011 at 06:38:52 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 2.127448 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): -20.17600 24.67300 ymin,ymax (A): -28.57100 11.16200 zmin,zma (A): -13.50300 36.69800 x,y,z range (A): 44.84900 39.73300 50.20100 scale (grids/A): 2.127448 object centre (A): 2.248501 -8.704500 11.59750 number of atom coordinates read : 2040 total number of charged atoms : 1906 net assigned charge : 6.931010 assigned positive charge : 309.1391 centred at (gu) : 89.68477 91.65878 88.41078 assigned negative charge : -302.2082 centred at (gu) : 89.12713 91.59081 88.32828 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16711 grid for indexing accessible points = 1.400000 m= 29286 mr = 52710 m= 5617 mr = 22222 m= 491 mr = 3677 m= 11 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 30321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15161 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) : 0.7091492 object centre at (A) : 2.248501 -8.704500 11.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4251907E-02 4.6321578E-02 midg,1,midg; midg,igrid,midg 4.4531543E-03 3.2802917E-02 1,midg,midg; igrid,midg,midg 1.3210577E-02 3.9365601E-02 gauss-seidel spectral radius is 0.9988307 estimated iterations to convergence 231 setup time was (sec) 0.8000000 now iterating at: 06:38:53 rms-change max change #iterations 4.543080 169.2322 at 10iterations 2.242072 88.82886 at 20iterations 1.116861 34.19997 at 30iterations 0.5531331 17.34106 at 40iterations 0.2751193 8.480549 at 50iterations 0.1367190 4.199467 at 60iterations 6.8018019E-02 2.031167 at 70iterations 3.3953179E-02 0.9570837 at 80iterations 1.6954226E-02 0.5225811 at 90iterations 8.5267778E-03 0.2556076 at 100iterations 4.2924439E-03 0.1375580 at 110iterations 2.2039292E-03 7.9727173E-02 at 120iterations finished qdiffx linear iterations at : 06:38:58 total time elapsed so far: 6.650000 # loops : 120 mean,max change (kT/e) : 2.2039292E-03 7.9727173E-02 energy calculations done at 6.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 06:38:59 6.814u 0.160s 0:07.48 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 Tue Oct 11 2011 at 06:38:59 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.191171 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): -20.17600 24.67300 ymin,ymax (A): -28.57100 11.16200 zmin,zma (A): -13.50300 36.69800 x,y,z range (A): 44.84900 39.73300 50.20100 scale (grids/A): 3.191171 object centre (A): 2.248501 -8.704500 11.59750 number of atom coordinates read : 2040 total number of charged atoms : 1906 net assigned charge : 6.931010 assigned positive charge : 309.1391 centred at (gu) : 89.52714 92.48820 87.61622 assigned negative charge : -302.2082 centred at (gu) : 88.69082 92.38622 87.49248 start vw surface at 0.1300000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 170051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16711 grid for indexing accessible points = 1.400000 m= 91678 mr = 126826 m= 36902 mr = 76238 m= 10446 mr = 30243 m= 2047 mr = 8016 m= 233 mr = 1490 m= 4 mr = 145 m= 0 mr = 2 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.650000 number of dielectric boundary points 68401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 15248 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) : 2.127448 object centre at (A) : 2.248501 -8.704500 11.59750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7105486 0.3666208 midg,1,midg; midg,igrid,midg 1.8225642E-02 0.2607643 1,midg,midg; igrid,midg,midg 0.2322248 0.2970774 gauss-seidel spectral radius is 0.9992907 estimated iterations to convergence 296 setup time was (sec) 1.950000 now iterating at: 06:39:01 rms-change max change #iterations 10.16433 378.5895 at 10iterations 6.005463 136.6626 at 20iterations 3.540053 72.97742 at 30iterations 2.084720 37.56189 at 40iterations 1.225438 24.03339 at 50iterations 0.7195202 14.59977 at 60iterations 0.4225099 7.820836 at 70iterations 0.2469949 4.724667 at 80iterations 0.1448692 2.709717 at 90iterations 8.4695652E-02 1.542969 at 100iterations 4.9676556E-02 0.9245052 at 110iterations 2.9244607E-02 0.4982452 at 120iterations 1.7344475E-02 0.2977982 at 130iterations 1.0404054E-02 0.2002411 at 140iterations 6.3872165E-03 0.1235657 at 150iterations 4.0572546E-03 7.6610565E-02 at 160iterations 2.7172868E-03 5.6221008E-02 at 170iterations 1.9198696E-03 3.7521362E-02 at 180iterations finished qdiffx linear iterations at : 06:39:11 total time elapsed so far: 11.41000 # loops : 180 mean,max change (kT/e) : 1.9198696E-03 3.7521362E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.60000 DelPhi exited at 06:39:11 11.601u 0.162s 0:12.26 95.9% 0+0k 0+0io 0pf+0w