Mon Oct 10 19:32:55 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 19:32:56 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2694 !!! WARNING: GLM 155 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5751676 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): -10.64600 38.02300 ymin,ymax (A): -7.048000 46.47400 zmin,zma (A): -10.40400 51.49100 x,y,z range (A): 48.66900 53.52200 61.89500 scale (grids/A): 0.5751676 object centre (A): 13.68850 19.71300 20.54350 number of atom coordinates read : 2694 total number of charged atoms : 2552 net assigned charge : 3.906021 assigned positive charge : 397.3206 centred at (gu) : 91.01041 91.10427 90.73415 assigned negative charge : -393.4157 centred at (gu) : 90.95119 91.22363 90.69961 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5941 nv = 96 ne = 84 npr = 53088 no. pairs analyzed = 53088 no. exposed pairs = 3811 no. arc points = 26706 no. surface atoms = 1252 nbur = 1442 mkacc time = 0.1300000 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 = 1.512000 m= 274 mr = 2865 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2645 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7544 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3554895E-10 1.5412160E-09 midg,1,midg; midg,igrid,midg 2.0616697E-09 -1.6756008E-09 1,midg,midg; igrid,midg,midg -1.9535253E-10 2.1600743E-09 gauss-seidel spectral radius is 0.9843854 estimated iterations to convergence 66 setup time was (sec) 0.6200000 now iterating at: 19:32:56 rms-change max change #iterations 8.7732218E-02 15.16171 at 10iterations 6.8081487E-03 1.180515 at 20iterations 5.5875594E-04 9.2452407E-02 at 30iterations 5.5494515E-05 8.7118149E-03 at 40iterations 8.3222403E-06 1.5945435E-03 at 50iterations finished qdiffx linear iterations at : 19:32:59 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 8.3222403E-06 1.5945435E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.730000 DelPhi exited at 19:33:00 3.730u 0.192s 0:04.45 88.0% 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 19:33:00 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2694 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.725503 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): -10.64600 38.02300 ymin,ymax (A): -7.048000 46.47400 zmin,zma (A): -10.40400 51.49100 x,y,z range (A): 48.66900 53.52200 61.89500 scale (grids/A): 1.725503 object centre (A): 13.68850 19.71300 20.54350 number of atom coordinates read : 2694 total number of charged atoms : 2552 net assigned charge : 3.906021 assigned positive charge : 397.3206 centred at (gu) : 93.03082 93.31243 92.20180 assigned negative charge : -393.4157 centred at (gu) : 92.85341 93.67066 92.09859 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 64499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26706 grid for indexing accessible points = 1.400000 m= 21063 mr = 41762 m= 2575 mr = 14203 m= 75 mr = 1283 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.5700000 number of dielectric boundary points 30965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 253 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19782 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) : 0.5751676 object centre at (A) : 13.68850 19.71300 20.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0147288E-02 2.6466412E-02 midg,1,midg; midg,igrid,midg 7.8846738E-03 -1.2765923E-02 1,midg,midg; igrid,midg,midg -1.6990385E-03 -2.2265443E-03 gauss-seidel spectral radius is 0.9983636 estimated iterations to convergence 196 setup time was (sec) 0.8900000 now iterating at: 19:33:01 rms-change max change #iterations 3.501822 181.9576 at 10iterations 1.509874 63.33453 at 20iterations 0.6565905 23.58516 at 30iterations 0.2861335 11.88582 at 40iterations 0.1243556 4.730246 at 50iterations 5.3939022E-02 1.864103 at 60iterations 2.3544503E-02 0.8397217 at 70iterations 1.0231473E-02 0.4048195 at 80iterations 4.4576810E-03 0.1583061 at 90iterations 1.9509537E-03 7.6764882E-02 at 100iterations 8.4908417E-04 3.0941963E-02 at 110iterations 3.7154675E-04 1.5331268E-02 at 120iterations finished qdiffx linear iterations at : 19:33:09 total time elapsed so far: 8.630000 # loops : 120 mean,max change (kT/e) : 3.7154675E-04 1.5331268E-02 energy calculations done at 8.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.850000 DelPhi exited at 19:33:10 8.857u 0.214s 0:09.97 90.8% 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 Mon Oct 10 2011 at 19:33:10 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2694 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.588254 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): -10.64600 38.02300 ymin,ymax (A): -7.048000 46.47400 zmin,zma (A): -10.40400 51.49100 x,y,z range (A): 48.66900 53.52200 61.89500 scale (grids/A): 2.588254 object centre (A): 13.68850 19.71300 20.54350 number of atom coordinates read : 2694 total number of charged atoms : 2552 net assigned charge : 3.906021 assigned positive charge : 397.3206 centred at (gu) : 94.54613 94.96854 93.30244 assigned negative charge : -393.4157 centred at (gu) : 94.28009 95.50597 93.14799 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 149546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26706 grid for indexing accessible points = 1.400000 m= 69619 mr = 102766 m= 22439 mr = 53866 m= 4222 mr = 16766 m= 332 mr = 2737 m= 2 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 905 time to turn everything in is 1.230000 number of dielectric boundary points 69901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 20393 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) : 1.725503 object centre at (A) : 13.68850 19.71300 20.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2267828 0.2436933 midg,1,midg; midg,igrid,midg 0.1557565 -8.2355119E-02 1,midg,midg; igrid,midg,midg -2.0219717E-02 -5.9972491E-02 gauss-seidel spectral radius is 0.9991976 estimated iterations to convergence 279 setup time was (sec) 1.560000 now iterating at: 19:33:12 rms-change max change #iterations 8.858062 312.0405 at 10iterations 5.085801 143.1251 at 20iterations 2.894060 77.23711 at 30iterations 1.645455 39.33195 at 40iterations 0.9330180 23.15422 at 50iterations 0.5250641 11.24017 at 60iterations 0.2961945 6.568477 at 70iterations 0.1670326 3.809933 at 80iterations 9.4152607E-02 1.908451 at 90iterations 5.2880634E-02 1.124664 at 100iterations 2.9672267E-02 0.6431866 at 110iterations 1.6659683E-02 0.3384056 at 120iterations 9.3667433E-03 0.1961098 at 130iterations 5.2456306E-03 0.1129646 at 140iterations 2.9456283E-03 5.9638977E-02 at 150iterations 1.6515617E-03 3.0714035E-02 at 160iterations 9.2550053E-04 1.9662857E-02 at 170iterations 5.2048889E-04 1.1004448E-02 at 180iterations finished qdiffx linear iterations at : 19:33:23 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 5.2048889E-04 1.1004448E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 19:33:24 12.824u 0.217s 0:13.70 95.1% 0+0k 0+0io 0pf+0w