Tue Oct 11 03:16:09 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 03:16:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 0.6331590 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 0.6331590 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 1.000010 assigned positive charge : 351.3182 centred at (gu) : 91.61993 91.32281 88.61367 assigned negative charge : -350.3189 centred at (gu) : 91.64699 91.20975 88.77338 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6525 nv = 96 ne = 84 npr = 48199 no. pairs analyzed = 48199 no. exposed pairs = 3046 no. arc points = 22119 no. surface atoms = 1023 nbur = 1370 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3457 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3200000 number of dielectric boundary points 3393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2239 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9683773E-08 -9.7358503E-09 midg,1,midg; midg,igrid,midg -6.7525368E-09 1.4144930E-08 1,midg,midg; igrid,midg,midg 2.2797386E-09 -2.1374806E-09 gauss-seidel spectral radius is 0.9870663 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 03:16:10 rms-change max change #iterations 0.1305386 21.05067 at 10iterations 1.2582092E-02 2.018074 at 20iterations 1.2124915E-03 0.1574923 at 30iterations 1.1581671E-04 1.6090393E-02 at 40iterations 1.1151904E-05 1.6555786E-03 at 50iterations finished qdiffx linear iterations at : 03:16:13 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.1151904E-05 1.6555786E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 03:16:14 4.051u 0.288s 0:04.64 93.3% 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 03:16:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 1.899477 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 1.899477 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 1.000010 assigned positive charge : 351.3182 centred at (gu) : 94.85930 93.96806 85.84070 assigned negative charge : -350.3189 centred at (gu) : 94.94087 93.62939 86.32018 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22119 grid for indexing accessible points = 1.400000 m= 25222 mr = 47539 m= 3826 mr = 18264 m= 200 mr = 2277 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 741 time to turn everything in is 0.6200000 number of dielectric boundary points 31305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 125 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 17660 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) : 0.6331590 object centre at (A) : -3.084499 -0.3605003 4.157001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3179637E-02 -6.1471056E-02 midg,1,midg; midg,igrid,midg -1.0378633E-02 8.9563308E-03 1,midg,midg; igrid,midg,midg 1.0712327E-02 -5.7997956E-04 gauss-seidel spectral radius is 0.9986078 estimated iterations to convergence 212 setup time was (sec) 0.9000000 now iterating at: 03:16:15 rms-change max change #iterations 3.962397 172.1296 at 10iterations 1.835279 66.76780 at 20iterations 0.8520873 27.92277 at 30iterations 0.3965011 14.32167 at 40iterations 0.1829226 5.908408 at 50iterations 8.5531898E-02 2.948658 at 60iterations 3.9605845E-02 1.292697 at 70iterations 1.8383533E-02 0.5812998 at 80iterations 8.5708378E-03 0.2910385 at 90iterations 3.9694547E-03 0.1244354 at 100iterations 1.8382147E-03 6.6969872E-02 at 110iterations 8.5712469E-04 3.1452179E-02 at 120iterations finished qdiffx linear iterations at : 03:16:24 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 8.5712469E-04 3.1452179E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.450000 DelPhi exited at 03:16:24 9.450u 0.336s 0:10.08 97.0% 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 Tue Oct 11 2011 at 03:16:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2393 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: 2.849216 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): -28.02200 21.85300 ymin,ymax (A): -24.85600 24.13500 zmin,zma (A): -23.95600 32.27000 x,y,z range (A): 49.87500 48.99100 56.22600 scale (grids/A): 2.849216 object centre (A): -3.084499 -0.3605003 4.157001 number of atom coordinates read : 2393 total number of charged atoms : 2248 net assigned charge : 1.000010 assigned positive charge : 351.3182 centred at (gu) : 97.28883 95.95183 83.76093 assigned negative charge : -350.3189 centred at (gu) : 97.41123 95.44399 84.48016 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22119 grid for indexing accessible points = 1.400000 m= 80415 mr = 114773 m= 29611 mr = 65144 m= 6840 mr = 23439 m= 836 mr = 4970 m= 32 mr = 485 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 2576 time to turn everything in is 1.610000 number of dielectric boundary points 70736 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 17983 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) : 1.899477 object centre at (A) : -3.084499 -0.3605003 4.157001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3221691 -0.7444922 midg,1,midg; midg,igrid,midg -8.7421894E-02 6.3361958E-02 1,midg,midg; igrid,midg,midg 0.1165510 -2.2878641E-02 gauss-seidel spectral radius is 0.9992537 estimated iterations to convergence 289 setup time was (sec) 1.920000 now iterating at: 03:16:26 rms-change max change #iterations 9.367298 361.2244 at 10iterations 5.435237 124.6938 at 20iterations 3.134441 96.27422 at 30iterations 1.805969 37.09565 at 40iterations 1.038391 21.17878 at 50iterations 0.5977221 12.66432 at 60iterations 0.3431119 7.458671 at 70iterations 0.1962843 3.926468 at 80iterations 0.1127477 2.151111 at 90iterations 6.4680502E-02 1.293674 at 100iterations 3.7061568E-02 0.7383547 at 110iterations 2.1242531E-02 0.4050915 at 120iterations 1.2140708E-02 0.2115173 at 130iterations 6.9561894E-03 0.1238410 at 140iterations 3.9843433E-03 7.2637558E-02 at 150iterations 2.2810663E-03 4.4981480E-02 at 160iterations 1.3058564E-03 2.6716232E-02 at 170iterations 7.4868440E-04 1.5849113E-02 at 180iterations finished qdiffx linear iterations at : 03:16:40 total time elapsed so far: 15.57000 # loops : 180 mean,max change (kT/e) : 7.4868440E-04 1.5849113E-02 energy calculations done at 15.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.76000 DelPhi exited at 03:16:41 15.762u 0.305s 0:16.54 97.0% 0+0k 0+0io 0pf+0w