Sat Oct 8 23:12:01 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 Sat Oct 8 2011 at 23:12:01 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 = 2443 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: 0.6590273 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): -28.29100 25.40300 ymin,ymax (A): -15.37400 27.78100 zmin,zma (A): -5.948000 48.07100 x,y,z range (A): 53.69400 43.15500 54.01900 scale (grids/A): 0.6590273 object centre (A): -1.444000 6.203500 21.06150 number of atom coordinates read : 2443 total number of charged atoms : 2307 net assigned charge : 11.00002 assigned positive charge : 356.5522 centred at (gu) : 90.65374 89.33370 88.61808 assigned negative charge : -345.5529 centred at (gu) : 90.64093 89.41866 88.62402 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7233 nv = 96 ne = 84 npr = 49019 no. pairs analyzed = 49019 no. exposed pairs = 3332 no. arc points = 23690 no. surface atoms = 1104 nbur = 1339 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 3657 m= 6 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7121890E-08 1.9764947E-08 midg,1,midg; midg,igrid,midg 4.7550007E-08 1.0898148E-08 1,midg,midg; igrid,midg,midg 2.1802004E-08 3.3356493E-08 gauss-seidel spectral radius is 0.9880610 estimated iterations to convergence 75 setup time was (sec) 0.5100000 now iterating at: 23:12:02 rms-change max change #iterations 0.1540324 24.15070 at 10iterations 1.6041448E-02 2.432453 at 20iterations 1.7799514E-03 0.2521305 at 30iterations 2.4368534E-04 3.8557053E-02 at 40iterations 5.1336494E-05 7.8144073E-03 at 50iterations finished qdiffx linear iterations at : 23:12:04 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 5.1336494E-05 7.8144073E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 23:12:05 3.116u 0.161s 0:03.59 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 Sat Oct 8 2011 at 23:12:05 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 = 2443 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: 1.977082 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): -28.29100 25.40300 ymin,ymax (A): -15.37400 27.78100 zmin,zma (A): -5.948000 48.07100 x,y,z range (A): 53.69400 43.15500 54.01900 scale (grids/A): 1.977082 object centre (A): -1.444000 6.203500 21.06150 number of atom coordinates read : 2443 total number of charged atoms : 2307 net assigned charge : 11.00002 assigned positive charge : 356.5522 centred at (gu) : 91.96101 88.00093 85.85364 assigned negative charge : -345.5529 centred at (gu) : 91.92274 88.25580 85.87208 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23690 grid for indexing accessible points = 1.400000 m= 28571 mr = 50571 m= 5375 mr = 20109 m= 381 mr = 3242 m= 8 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 18209 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) : 0.6590273 object centre at (A) : -1.444000 6.203500 21.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3702763E-02 4.5687139E-02 midg,1,midg; midg,igrid,midg 3.2300439E-02 3.7838200E-03 1,midg,midg; igrid,midg,midg 2.5089769E-02 6.6741221E-02 gauss-seidel spectral radius is 0.9987263 estimated iterations to convergence 222 setup time was (sec) 0.8200000 now iterating at: 23:12:06 rms-change max change #iterations 4.252725 236.2249 at 10iterations 2.041255 73.43116 at 20iterations 0.9758471 33.35265 at 30iterations 0.4695171 14.95717 at 40iterations 0.2240963 7.703485 at 50iterations 0.1070072 3.531500 at 60iterations 5.1683106E-02 1.636894 at 70iterations 2.4826108E-02 0.7701716 at 80iterations 1.1910228E-02 0.3654346 at 90iterations 5.7413788E-03 0.1837311 at 100iterations 2.7686022E-03 8.6649895E-02 at 110iterations 1.3338544E-03 4.3767929E-02 at 120iterations finished qdiffx linear iterations at : 23:12:12 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.3338544E-03 4.3767929E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 23:12:12 7.099u 0.167s 0:07.56 95.8% 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 Sat Oct 8 2011 at 23:12:12 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 = 2443 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: 2.965623 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): -28.29100 25.40300 ymin,ymax (A): -15.37400 27.78100 zmin,zma (A): -5.948000 48.07100 x,y,z range (A): 53.69400 43.15500 54.01900 scale (grids/A): 2.965623 object centre (A): -1.444000 6.203500 21.06150 number of atom coordinates read : 2443 total number of charged atoms : 2307 net assigned charge : 11.00002 assigned positive charge : 356.5522 centred at (gu) : 92.94136 87.00121 83.78030 assigned negative charge : -345.5529 centred at (gu) : 92.88407 87.38372 83.80799 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 176180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23690 grid for indexing accessible points = 1.400000 m= 88843 mr = 123143 m= 35035 mr = 70345 m= 9892 mr = 27322 m= 1731 mr = 7168 m= 125 mr = 1147 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.380000 number of dielectric boundary points 82645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 18455 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) : 1.977082 object centre at (A) : -1.444000 6.203500 21.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2489506 0.6244009 midg,1,midg; midg,igrid,midg 0.2913169 -3.1840813E-03 1,midg,midg; igrid,midg,midg 0.2288979 0.5365528 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 1.660000 now iterating at: 23:12:14 rms-change max change #iterations 10.15463 377.6592 at 10iterations 6.121822 150.8060 at 20iterations 3.645716 94.62131 at 30iterations 2.159744 43.05886 at 40iterations 1.278684 28.23146 at 50iterations 0.7552290 14.96143 at 60iterations 0.4438573 8.953266 at 70iterations 0.2606739 4.975333 at 80iterations 0.1526555 3.067349 at 90iterations 8.9690775E-02 1.603755 at 100iterations 5.2393723E-02 1.045036 at 110iterations 3.0689202E-02 0.5235558 at 120iterations 1.7929377E-02 0.3337116 at 130iterations 1.0472205E-02 0.1918640 at 140iterations 6.1257370E-03 0.1068573 at 150iterations 3.5899382E-03 6.4336777E-02 at 160iterations 2.1121777E-03 3.9415359E-02 at 170iterations 1.2469396E-03 2.2120908E-02 at 180iterations finished qdiffx linear iterations at : 23:12:24 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 1.2469396E-03 2.2120908E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 23:12:24 11.557u 0.182s 0:12.00 97.7% 0+0k 0+0io 0pf+0w