Mon Oct 10 17:04:33 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 Mon Oct 10 2011 at 17:04:33 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2864 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6156613 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): -8.605000 48.75300 ymin,ymax (A): -7.814000 39.24600 zmin,zma (A): -1.195000 56.62900 x,y,z range (A): 57.35800 47.06000 57.82400 scale (grids/A): 0.6156613 object centre (A): 20.07400 15.71600 27.71700 number of atom coordinates read : 2864 total number of charged atoms : 2723 net assigned charge : -4.485977 assigned positive charge : 433.7430 centred at (gu) : 89.09110 89.44596 88.79278 assigned negative charge : -438.2302 centred at (gu) : 88.99715 89.32308 88.70887 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7285 nv = 96 ne = 84 npr = 57173 no. pairs analyzed = 57173 no. exposed pairs = 3745 no. arc points = 26109 no. surface atoms = 1265 nbur = 1599 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 336 mr = 3815 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3500000 number of dielectric boundary points 3795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 256 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1178649E-08 1.8929891E-09 midg,1,midg; midg,igrid,midg -1.2637960E-08 4.4268762E-09 1,midg,midg; igrid,midg,midg -1.1284865E-08 2.5612945E-09 gauss-seidel spectral radius is 0.9863680 estimated iterations to convergence 70 setup time was (sec) 0.6500000 now iterating at: 17:04:35 rms-change max change #iterations 0.1296663 21.15350 at 10iterations 1.1639841E-02 2.108973 at 20iterations 1.0486149E-03 0.1570582 at 30iterations 9.6290467E-05 1.2326241E-02 at 40iterations 8.9461601E-06 1.3275146E-03 at 50iterations finished qdiffx linear iterations at : 17:04:39 total time elapsed so far: 4.740000 # loops : 50 mean,max change (kT/e) : 8.9461601E-06 1.3275146E-03 energy calculations done at 4.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.910000 DelPhi exited at 17:04:39 4.914u 0.386s 0:05.81 91.0% 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 Mon Oct 10 2011 at 17:04:39 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2864 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.846984 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): -8.605000 48.75300 ymin,ymax (A): -7.814000 39.24600 zmin,zma (A): -1.195000 56.62900 x,y,z range (A): 57.35800 47.06000 57.82400 scale (grids/A): 1.846984 object centre (A): 20.07400 15.71600 27.71700 number of atom coordinates read : 2864 total number of charged atoms : 2723 net assigned charge : -4.485977 assigned positive charge : 433.7430 centred at (gu) : 87.27254 88.33710 86.37766 assigned negative charge : -438.2302 centred at (gu) : 86.99113 87.96896 86.12627 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 79733 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26109 grid for indexing accessible points = 1.400000 m= 26487 mr = 54389 m= 3316 mr = 18496 m= 134 mr = 1719 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1425 time to turn everything in is 0.6300000 number of dielectric boundary points 35053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21367 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) : 0.6156613 object centre at (A) : 20.07400 15.71600 27.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6044212E-03 1.8124631E-02 midg,1,midg; midg,igrid,midg -2.4384663E-02 -1.7601445E-03 1,midg,midg; igrid,midg,midg -5.0259028E-02 2.3132298E-02 gauss-seidel spectral radius is 0.9985815 estimated iterations to convergence 210 setup time was (sec) 0.9800000 now iterating at: 17:04:41 rms-change max change #iterations 4.280796 177.3748 at 10iterations 1.963655 65.11125 at 20iterations 0.9067425 27.83739 at 30iterations 0.4163986 13.13835 at 40iterations 0.1915289 6.032191 at 50iterations 8.8496387E-02 2.799894 at 60iterations 4.0776353E-02 1.310258 at 70iterations 1.8826229E-02 0.5498495 at 80iterations 8.6682756E-03 0.2765408 at 90iterations 4.0009767E-03 0.1213341 at 100iterations 1.8450554E-03 6.0580254E-02 at 110iterations 8.5287122E-04 2.6006699E-02 at 120iterations finished qdiffx linear iterations at : 17:04:51 total time elapsed so far: 11.64000 # loops : 120 mean,max change (kT/e) : 8.5287122E-04 2.6006699E-02 energy calculations done at 11.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.81000 DelPhi exited at 17:04:52 11.812u 0.477s 0:12.99 94.5% 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 Mon Oct 10 2011 at 17:04:52 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2864 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.770476 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): -8.605000 48.75300 ymin,ymax (A): -7.814000 39.24600 zmin,zma (A): -1.195000 56.62900 x,y,z range (A): 57.35800 47.06000 57.82400 scale (grids/A): 2.770476 object centre (A): 20.07400 15.71600 27.71700 number of atom coordinates read : 2864 total number of charged atoms : 2723 net assigned charge : -4.485977 assigned positive charge : 433.7430 centred at (gu) : 85.90849 87.50536 84.56633 assigned negative charge : -438.2302 centred at (gu) : 85.48643 86.95332 84.18938 start vw surface at 0.1200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 184788 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26109 grid for indexing accessible points = 1.400000 m= 88135 mr = 132267 m= 28475 mr = 70480 m= 5473 mr = 21703 m= 520 mr = 3623 m= 10 mr = 243 m= 0 mr = 3 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 4970 time to turn everything in is 1.680000 number of dielectric boundary points 79082 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 21778 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) : 1.846984 object centre at (A) : 20.07400 15.71600 27.71700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2171247 0.4327390 midg,1,midg; midg,igrid,midg -0.2135816 -6.6426955E-02 1,midg,midg; igrid,midg,midg -0.6199127 0.3271905 gauss-seidel spectral radius is 0.9992620 estimated iterations to convergence 290 setup time was (sec) 2.100000 now iterating at: 17:04:55 rms-change max change #iterations 10.42600 307.8891 at 10iterations 6.186446 149.6117 at 20iterations 3.636386 83.71149 at 30iterations 2.123760 50.01335 at 40iterations 1.236040 25.30898 at 50iterations 0.7166377 14.36553 at 60iterations 0.4154512 7.898003 at 70iterations 0.2403576 4.748901 at 80iterations 0.1388894 2.787104 at 90iterations 8.0159411E-02 1.711011 at 100iterations 4.6174616E-02 0.8864050 at 110iterations 2.6662858E-02 0.4619136 at 120iterations 1.5363762E-02 0.2721553 at 130iterations 8.8372622E-03 0.1572938 at 140iterations 5.0902152E-03 9.1157436E-02 at 150iterations 2.9298519E-03 5.0794601E-02 at 160iterations 1.6879989E-03 3.1894684E-02 at 170iterations 9.6999935E-04 1.8054962E-02 at 180iterations finished qdiffx linear iterations at : 17:05:12 total time elapsed so far: 18.58000 # loops : 180 mean,max change (kT/e) : 9.6999935E-04 1.8054962E-02 energy calculations done at 18.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.75000 DelPhi exited at 17:05:13 18.755u 0.446s 0:20.73 92.5% 0+0k 0+0io 0pf+0w