Tue Oct 11 04:19:28 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 04:19:28 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6628929 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): -14.72000 29.59000 ymin,ymax (A): 7.576000 51.81300 zmin,zma (A): 25.83300 79.53699 x,y,z range (A): 44.31000 44.23700 53.70399 scale (grids/A): 0.6628929 object centre (A): 7.435000 29.69450 52.68500 number of atom coordinates read : 2543 total number of charged atoms : 2394 net assigned charge : 4.162024 assigned positive charge : 379.4759 centred at (gu) : 90.67989 90.93970 88.95541 assigned negative charge : -375.3146 centred at (gu) : 90.99797 90.68096 89.08736 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7501 nv = 96 ne = 84 npr = 52430 no. pairs analyzed = 52430 no. exposed pairs = 3083 no. arc points = 21207 no. surface atoms = 1041 nbur = 1502 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 476 mr = 4331 m= 1 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.3300000 number of dielectric boundary points 3577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2021 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8785 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7276909E-08 -1.2938989E-08 midg,1,midg; midg,igrid,midg -3.5522071E-08 7.6780196E-08 1,midg,midg; igrid,midg,midg 6.4637618E-08 -6.5294991E-08 gauss-seidel spectral radius is 0.9881971 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 04:19:29 rms-change max change #iterations 0.1696493 24.61652 at 10iterations 1.8578768E-02 2.482788 at 20iterations 2.0732207E-03 0.2501106 at 30iterations 2.8405746E-04 3.8276672E-02 at 40iterations 5.9511647E-05 8.2092285E-03 at 50iterations finished qdiffx linear iterations at : 04:19:32 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 5.9511647E-05 8.2092285E-03 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 04:19:33 3.617u 0.205s 0:04.30 88.6% 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 04:19:33 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.988679 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): -14.72000 29.59000 ymin,ymax (A): 7.576000 51.81300 zmin,zma (A): 25.83300 79.53699 x,y,z range (A): 44.31000 44.23700 53.70399 scale (grids/A): 1.988679 object centre (A): 7.435000 29.69450 52.68500 number of atom coordinates read : 2543 total number of charged atoms : 2394 net assigned charge : 4.162024 assigned positive charge : 379.4759 centred at (gu) : 92.03928 92.81874 86.86594 assigned negative charge : -375.3146 centred at (gu) : 92.99366 92.04291 87.26214 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21207 grid for indexing accessible points = 1.400000 m= 31257 mr = 57881 m= 5320 mr = 23558 m= 360 mr = 3501 m= 8 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 1302 time to turn everything in is 0.6100000 number of dielectric boundary points 32982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 18915 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) : 0.6628929 object centre at (A) : 7.435000 29.69450 52.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8432064E-02 -2.3871396E-02 midg,1,midg; midg,igrid,midg -1.2368989E-02 5.6549322E-02 1,midg,midg; igrid,midg,midg 5.8791190E-02 -5.0925709E-02 gauss-seidel spectral radius is 0.9987364 estimated iterations to convergence 223 setup time was (sec) 0.8900000 now iterating at: 04:19:34 rms-change max change #iterations 4.534011 200.2178 at 10iterations 2.191936 69.62965 at 20iterations 1.054562 33.69476 at 30iterations 0.5096197 16.82857 at 40iterations 0.2460191 7.986575 at 50iterations 0.1185823 3.487194 at 60iterations 5.7466190E-02 1.775876 at 70iterations 2.7744122E-02 0.8233299 at 80iterations 1.3388558E-02 0.3930092 at 90iterations 6.4607491E-03 0.2080307 at 100iterations 3.1426041E-03 9.8137856E-02 at 110iterations 1.5215526E-03 4.7180176E-02 at 120iterations finished qdiffx linear iterations at : 04:19:40 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.5215526E-03 4.7180176E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 04:19:41 7.550u 0.207s 0:08.06 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 Tue Oct 11 2011 at 04:19:41 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2543 !!! 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: 2.983018 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): -14.72000 29.59000 ymin,ymax (A): 7.576000 51.81300 zmin,zma (A): 25.83300 79.53699 x,y,z range (A): 44.31000 44.23700 53.70399 scale (grids/A): 2.983018 object centre (A): 7.435000 29.69450 52.68500 number of atom coordinates read : 2543 total number of charged atoms : 2394 net assigned charge : 4.162024 assigned positive charge : 379.4759 centred at (gu) : 93.05871 94.22799 85.29874 assigned negative charge : -375.3146 centred at (gu) : 94.49042 93.06431 85.89303 start vw surface at 0.1800000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 187354 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21207 grid for indexing accessible points = 1.400000 m= 99178 mr = 139393 m= 38065 mr = 82607 m= 9736 mr = 31084 m= 1601 mr = 7456 m= 117 mr = 1105 m= 2 mr = 61 m= 0 mr = 2 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 4593 time to turn everything in is 1.590000 number of dielectric boundary points 74345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19140 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) : 1.988679 object centre at (A) : 7.435000 29.69450 52.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5479081 -0.1082475 midg,1,midg; midg,igrid,midg -0.1250472 0.4721840 1,midg,midg; igrid,midg,midg 0.4956275 -0.5648605 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 1.920000 now iterating at: 04:19:43 rms-change max change #iterations 10.40108 367.9827 at 10iterations 6.122404 148.2465 at 20iterations 3.594140 64.96446 at 30iterations 2.106534 44.69217 at 40iterations 1.231501 28.43189 at 50iterations 0.7184439 14.05095 at 60iterations 0.4183052 7.416732 at 70iterations 0.2435532 4.554090 at 80iterations 0.1419531 2.434956 at 90iterations 8.2526825E-02 1.503605 at 100iterations 4.8011817E-02 0.8743801 at 110iterations 2.7918275E-02 0.5044975 at 120iterations 1.6253861E-02 0.2840004 at 130iterations 9.4829267E-03 0.1665020 at 140iterations 5.5336449E-03 0.1043854 at 150iterations 3.2612009E-03 5.8753014E-02 at 160iterations 1.9468304E-03 3.7250519E-02 at 170iterations 1.1830273E-03 2.1011353E-02 at 180iterations finished qdiffx linear iterations at : 04:19:53 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 1.1830273E-03 2.1011353E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 04:19:54 12.167u 0.200s 0:13.13 94.1% 0+0k 0+0io 0pf+0w