Sun Oct 9 15:06:14 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 Sun Oct 9 2011 at 15:06:14 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 = 5668 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: 0.5052655 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): -17.64800 52.81000 ymin,ymax (A): 98.53300 167.9090 zmin,zma (A): -34.66100 31.55000 x,y,z range (A): 70.45800 69.37600 66.21101 scale (grids/A): 0.5052655 object centre (A): 17.58100 133.2210 -1.555501 number of atom coordinates read : 5668 total number of charged atoms : 5492 net assigned charge : -4.999957 assigned positive charge : 870.2483 centred at (gu) : 89.96235 88.92062 88.75238 assigned negative charge : -875.2556 centred at (gu) : 89.95139 88.99138 88.72647 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8802 nv = 96 ne = 84 npr = 117257 no. pairs analyzed = 117257 no. exposed pairs = 6461 no. arc points = 43989 no. surface atoms = 2182 nbur = 3486 mkacc time = 0.2800000 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 = 1.708000 m= 306 mr = 4909 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.5300000 number of dielectric boundary points 4195 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4219 ## 593 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 11893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7068069E-10 5.2522153E-12 midg,1,midg; midg,igrid,midg 1.6136142E-10 -1.7768910E-10 1,midg,midg; igrid,midg,midg -8.5327030E-11 -2.9045861E-11 gauss-seidel spectral radius is 0.9800146 estimated iterations to convergence 58 setup time was (sec) 0.7600000 now iterating at: 15:06:15 rms-change max change #iterations 7.0988029E-02 11.23738 at 10iterations 5.4958286E-03 0.7896690 at 20iterations 1.0079935E-03 0.1741219 at 30iterations 2.5364727E-04 4.1694641E-02 at 40iterations 6.5677566E-05 1.0585785E-02 at 50iterations finished qdiffx linear iterations at : 15:06:17 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 6.5677566E-05 1.0585785E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 15:06:18 3.612u 0.173s 0:04.11 91.9% 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 15:06:18 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 = 5668 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.515797 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): -17.64800 52.81000 ymin,ymax (A): 98.53300 167.9090 zmin,zma (A): -34.66100 31.55000 x,y,z range (A): 70.45800 69.37600 66.21101 scale (grids/A): 1.515797 object centre (A): 17.58100 133.2210 -1.555501 number of atom coordinates read : 5668 total number of charged atoms : 5492 net assigned charge : -4.999957 assigned positive charge : 870.2483 centred at (gu) : 89.88557 86.76020 86.25543 assigned negative charge : -875.2556 centred at (gu) : 89.85427 86.97360 86.17905 start vw surface at 0.2400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 100873 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43989 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 28693 mr = 72063 m= 2391 mr = 19810 m= 44 mr = 1001 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 2947 time to turn everything in is 0.7400000 number of dielectric boundary points 39127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 610 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 41073 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) : 0.5052655 object centre at (A) : 17.58100 133.2210 -1.555501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9547664E-03 -6.2392140E-03 midg,1,midg; midg,igrid,midg 2.1214107E-02 -1.0493352E-02 1,midg,midg; igrid,midg,midg -2.4249852E-02 -1.0851289E-02 gauss-seidel spectral radius is 0.9981185 estimated iterations to convergence 183 setup time was (sec) 1.040000 now iterating at: 15:06:19 rms-change max change #iterations 4.157845 156.1451 at 10iterations 1.709239 52.89149 at 20iterations 0.7042464 23.41562 at 30iterations 0.2893927 9.339271 at 40iterations 0.1198348 3.548481 at 50iterations 4.9446780E-02 1.640944 at 60iterations 2.0487098E-02 0.6599903 at 70iterations 8.5685281E-03 0.2522364 at 80iterations 3.6337799E-03 0.1178818 at 90iterations 1.5760824E-03 4.7126770E-02 at 100iterations 7.0799678E-04 2.4808884E-02 at 110iterations 3.3744736E-04 1.2016296E-02 at 120iterations finished qdiffx linear iterations at : 15:06:26 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 3.3744736E-04 1.2016296E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 15:06:26 8.011u 0.162s 0:08.44 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 15:06:26 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 = 5668 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.273695 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): -17.64800 52.81000 ymin,ymax (A): 98.53300 167.9090 zmin,zma (A): -34.66100 31.55000 x,y,z range (A): 70.45800 69.37600 66.21101 scale (grids/A): 2.273695 object centre (A): 17.58100 133.2210 -1.555501 number of atom coordinates read : 5668 total number of charged atoms : 5492 net assigned charge : -4.999957 assigned positive charge : 870.2483 centred at (gu) : 89.82764 85.13984 84.38268 assigned negative charge : -875.2556 centred at (gu) : 89.78152 85.46030 84.26842 start vw surface at 0.2300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 235501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43989 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 104556 mr = 176428 m= 25954 mr = 83391 m= 3448 mr = 19258 m= 136 mr = 2119 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 9945 time to turn everything in is 1.750000 number of dielectric boundary points 88365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 43810 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) : 1.515797 object centre at (A) : 17.58100 133.2210 -1.555501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2681242 -0.1743337 midg,1,midg; midg,igrid,midg 0.5045550 -0.1992521 1,midg,midg; igrid,midg,midg -0.3572197 -0.2554911 gauss-seidel spectral radius is 0.9991677 estimated iterations to convergence 274 setup time was (sec) 2.060000 now iterating at: 15:06:29 rms-change max change #iterations 11.14007 265.9757 at 10iterations 6.352570 135.3616 at 20iterations 3.593593 73.70866 at 30iterations 2.024584 41.76551 at 40iterations 1.137597 27.36536 at 50iterations 0.6371095 12.30767 at 60iterations 0.3566418 7.287704 at 70iterations 0.1990640 3.879721 at 80iterations 0.1111315 2.182625 at 90iterations 6.1963651E-02 1.232031 at 100iterations 3.4584023E-02 0.6039505 at 110iterations 1.9272368E-02 0.3530388 at 120iterations 1.0734857E-02 0.1906738 at 130iterations 5.9813149E-03 0.1248837 at 140iterations 3.3394033E-03 6.0356140E-02 at 150iterations 1.8626230E-03 3.3407211E-02 at 160iterations 1.0442528E-03 1.7391205E-02 at 170iterations 5.8650417E-04 1.0086060E-02 at 180iterations finished qdiffx linear iterations at : 15:06:39 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 5.8650417E-04 1.0086060E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 15:06:40 12.963u 0.189s 0:13.43 97.8% 0+0k 0+0io 0pf+0w