Sun Oct 9 08:17:42 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 08:17:42 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5677 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: 0.4845845 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): 17.13400 84.09500 ymin,ymax (A): 19.08500 85.74000 zmin,zma (A): -5.173000 68.29200 x,y,z range (A): 66.96100 66.65500 73.46500 scale (grids/A): 0.4845845 object centre (A): 50.61450 52.41250 31.55950 number of atom coordinates read : 5677 total number of charged atoms : 5510 net assigned charge : -6.999976 assigned positive charge : 851.0717 centred at (gu) : 90.14278 89.20559 91.39762 assigned negative charge : -858.0788 centred at (gu) : 90.12995 89.23804 91.45766 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8396 nv = 96 ne = 84 npr = 112834 no. pairs analyzed = 112834 no. exposed pairs = 7455 no. arc points = 51103 no. surface atoms = 2505 nbur = 3172 mkacc time = 0.2400000 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 = 1.764000 m= 280 mr = 4160 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.5000000 number of dielectric boundary points 4516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4776 ## 756 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11335 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9151134E-11 -1.2836161E-10 midg,1,midg; midg,igrid,midg 3.4791842E-12 -4.8245463E-11 1,midg,midg; igrid,midg,midg -3.9401551E-11 -1.6869537E-11 gauss-seidel spectral radius is 0.9783012 estimated iterations to convergence 56 setup time was (sec) 0.7300000 now iterating at: 08:17:43 rms-change max change #iterations 5.6722391E-02 10.35062 at 10iterations 3.0912049E-03 0.4674530 at 20iterations 3.8744099E-04 9.7909927E-02 at 30iterations 1.0143198E-04 2.6414871E-02 at 40iterations 2.9776160E-05 7.4748993E-03 at 50iterations finished qdiffx linear iterations at : 08:17:45 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.9776160E-05 7.4748993E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 08:17:46 3.352u 0.134s 0:03.78 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 08:17:46 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5677 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: 1.453754 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): 17.13400 84.09500 ymin,ymax (A): 19.08500 85.74000 zmin,zma (A): -5.173000 68.29200 x,y,z range (A): 66.96100 66.65500 73.46500 scale (grids/A): 1.453754 object centre (A): 50.61450 52.41250 31.55950 number of atom coordinates read : 5677 total number of charged atoms : 5510 net assigned charge : -6.999976 assigned positive charge : 851.0717 centred at (gu) : 90.42655 87.61446 94.19121 assigned negative charge : -858.0788 centred at (gu) : 90.38956 87.71402 94.37282 start vw surface at 0.2100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 95066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51103 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26468 mr = 63789 m= 1865 mr = 16747 m= 25 mr = 591 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1295 time to turn everything in is 0.6600000 number of dielectric boundary points 42297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 789 ## 16 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 40512 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) : 0.4845845 object centre at (A) : 50.61450 52.41250 31.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2525630E-03 -2.5564287E-02 midg,1,midg; midg,igrid,midg -1.1404322E-03 -8.6892862E-03 1,midg,midg; igrid,midg,midg -7.3445513E-04 -3.6958330E-03 gauss-seidel spectral radius is 0.9979734 estimated iterations to convergence 177 setup time was (sec) 0.9300000 now iterating at: 08:17:47 rms-change max change #iterations 3.716622 148.7608 at 10iterations 1.471508 48.59620 at 20iterations 0.5847532 18.17854 at 30iterations 0.2326552 7.536072 at 40iterations 9.2569791E-02 3.183136 at 50iterations 3.6955886E-02 1.129097 at 60iterations 1.4744476E-02 0.5260448 at 70iterations 5.9372042E-03 0.2050953 at 80iterations 2.4237731E-03 7.7621460E-02 at 90iterations 1.0369280E-03 3.8463354E-02 at 100iterations 4.7412951E-04 1.9077301E-02 at 110iterations 2.4417002E-04 1.0555267E-02 at 120iterations finished qdiffx linear iterations at : 08:17:53 total time elapsed so far: 7.000000 # loops : 120 mean,max change (kT/e) : 2.4417002E-04 1.0555267E-02 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 08:17:53 7.178u 0.159s 0:07.61 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 08:17:53 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5677 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.180630 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): 17.13400 84.09500 ymin,ymax (A): 19.08500 85.74000 zmin,zma (A): -5.173000 68.29200 x,y,z range (A): 66.96100 66.65500 73.46500 scale (grids/A): 2.180630 object centre (A): 50.61450 52.41250 31.55950 number of atom coordinates read : 5677 total number of charged atoms : 5510 net assigned charge : -6.999976 assigned positive charge : 851.0717 centred at (gu) : 90.63951 86.42135 96.28632 assigned negative charge : -858.0788 centred at (gu) : 90.58430 86.57096 96.55920 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 221444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51103 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96816 mr = 157528 m= 22276 mr = 73429 m= 2431 mr = 15245 m= 66 mr = 1220 m= 0 mr = 6 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 4588 time to turn everything in is 1.570000 number of dielectric boundary points 95605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 43849 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) : 1.453754 object centre at (A) : 50.61450 52.41250 31.55950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9906772E-02 -0.8296307 midg,1,midg; midg,igrid,midg -1.5083059E-02 -0.1743435 1,midg,midg; igrid,midg,midg 7.3293671E-02 -5.2655160E-02 gauss-seidel spectral radius is 0.9991530 estimated iterations to convergence 271 setup time was (sec) 1.850000 now iterating at: 08:17:55 rms-change max change #iterations 10.54340 289.6755 at 10iterations 6.081449 146.7553 at 20iterations 3.471312 78.08895 at 30iterations 1.973514 45.35465 at 40iterations 1.116874 23.56993 at 50iterations 0.6307418 12.41612 at 60iterations 0.3546534 7.565048 at 70iterations 0.1992288 4.540685 at 80iterations 0.1113839 2.203403 at 90iterations 6.2343989E-02 1.246750 at 100iterations 3.4760516E-02 0.6739073 at 110iterations 1.9388933E-02 0.3910418 at 120iterations 1.0832363E-02 0.2242546 at 130iterations 6.0402527E-03 0.1245537 at 140iterations 3.3650324E-03 6.0441971E-02 at 150iterations 1.8840195E-03 3.8412094E-02 at 160iterations 1.0589405E-03 1.9916534E-02 at 170iterations 5.9827004E-04 1.1349678E-02 at 180iterations finished qdiffx linear iterations at : 08:18:05 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 5.9827004E-04 1.1349678E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 08:18:06 11.848u 0.167s 0:12.33 97.3% 0+0k 0+0io 0pf+0w