Sun Oct 9 23:55:05 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 23:55:05 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 = 2490 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: 0.6235768 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): -7.693000 49.39700 ymin,ymax (A): -25.55400 22.02900 zmin,zma (A): -8.497000 40.46100 x,y,z range (A): 57.09000 47.58300 48.95800 scale (grids/A): 0.6235768 object centre (A): 20.85200 -1.762500 15.98200 number of atom coordinates read : 2490 total number of charged atoms : 2423 net assigned charge : 3.000007 assigned positive charge : 386.9839 centred at (gu) : 89.61850 90.35156 88.10506 assigned negative charge : -383.9847 centred at (gu) : 89.51978 90.41098 88.10559 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6346 nv = 96 ne = 84 npr = 49095 no. pairs analyzed = 49095 no. exposed pairs = 3146 no. arc points = 22179 no. surface atoms = 1062 nbur = 1428 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3405 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.3100000 number of dielectric boundary points 3241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2281 ## 236 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8043 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1604755E-09 1.8125565E-09 midg,1,midg; midg,igrid,midg 6.5005201E-09 -1.7539779E-09 1,midg,midg; igrid,midg,midg -4.9314202E-09 9.0341477E-09 gauss-seidel spectral radius is 0.9866703 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 23:55:06 rms-change max change #iterations 0.1246591 19.85793 at 10iterations 1.1456287E-02 2.038151 at 20iterations 1.0829101E-03 0.1597233 at 30iterations 1.0152698E-04 1.5567303E-02 at 40iterations 9.3677918E-06 1.6021729E-03 at 50iterations finished qdiffx linear iterations at : 23:55:09 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 9.3677918E-06 1.6021729E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 23:55:09 3.564u 0.185s 0:04.19 89.2% 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 23:55:09 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 = 2490 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: 1.870730 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): -7.693000 49.39700 ymin,ymax (A): -25.55400 22.02900 zmin,zma (A): -8.497000 40.46100 x,y,z range (A): 57.09000 47.58300 48.95800 scale (grids/A): 1.870730 object centre (A): 20.85200 -1.762500 15.98200 number of atom coordinates read : 2490 total number of charged atoms : 2423 net assigned charge : 3.000007 assigned positive charge : 386.9839 centred at (gu) : 88.85493 91.05408 84.31464 assigned negative charge : -383.9847 centred at (gu) : 88.55947 91.23299 84.31663 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22179 grid for indexing accessible points = 1.400000 m= 23354 mr = 47897 m= 2884 mr = 16767 m= 92 mr = 1618 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1717 time to turn everything in is 0.5200000 number of dielectric boundary points 29789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19057 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) : 0.6235768 object centre at (A) : 20.85200 -1.762500 15.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7920500E-02 3.3471640E-04 midg,1,midg; midg,igrid,midg 3.0585581E-03 5.1165563E-03 1,midg,midg; igrid,midg,midg -2.9566957E-02 3.4076855E-02 gauss-seidel spectral radius is 0.9985684 estimated iterations to convergence 210 setup time was (sec) 0.8300000 now iterating at: 23:55:10 rms-change max change #iterations 4.015382 176.5720 at 10iterations 1.847339 67.66724 at 20iterations 0.8487192 29.63836 at 30iterations 0.3897021 14.32772 at 40iterations 0.1791477 6.474526 at 50iterations 8.2447730E-02 2.827484 at 60iterations 3.7667759E-02 1.306271 at 70iterations 1.7349532E-02 0.5772972 at 80iterations 7.9838429E-03 0.2622595 at 90iterations 3.6709674E-03 0.1375504 at 100iterations 1.6896812E-03 5.4348707E-02 at 110iterations 7.7691796E-04 2.5382996E-02 at 120iterations finished qdiffx linear iterations at : 23:55:17 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 7.7691796E-04 2.5382996E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.980000 DelPhi exited at 23:55:18 7.985u 0.199s 0:08.60 95.0% 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 Sun Oct 9 2011 at 23:55:18 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 = 2490 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.806096 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): -7.693000 49.39700 ymin,ymax (A): -25.55400 22.02900 zmin,zma (A): -8.497000 40.46100 x,y,z range (A): 57.09000 47.58300 48.95800 scale (grids/A): 2.806096 object centre (A): 20.85200 -1.762500 15.98200 number of atom coordinates read : 2490 total number of charged atoms : 2423 net assigned charge : 3.000007 assigned positive charge : 386.9839 centred at (gu) : 88.28214 91.58090 81.47191 assigned negative charge : -383.9847 centred at (gu) : 87.83914 91.84943 81.47492 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 161378 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22179 grid for indexing accessible points = 1.400000 m= 77985 mr = 116022 m= 25178 mr = 63255 m= 4990 mr = 19740 m= 467 mr = 3511 m= 10 mr = 255 m= 0 mr = 2 time to grow re-entrant surface = 0.7499999 no. cavity mid-points inaccessible to solvent = 5534 time to turn everything in is 1.330000 number of dielectric boundary points 67223 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 19383 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) : 1.870730 object centre at (A) : 20.85200 -1.762500 15.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1813464 -7.1238321E-03 midg,1,midg; midg,igrid,midg 2.9317841E-02 0.1119466 1,midg,midg; igrid,midg,midg -0.4923990 0.3908768 gauss-seidel spectral radius is 0.9992452 estimated iterations to convergence 287 setup time was (sec) 1.660000 now iterating at: 23:55:20 rms-change max change #iterations 9.456615 357.4166 at 10iterations 5.436186 116.9076 at 20iterations 3.098168 65.81529 at 30iterations 1.770693 34.92279 at 40iterations 1.011251 18.90567 at 50iterations 0.5761347 11.30511 at 60iterations 0.3281184 7.516063 at 70iterations 0.1868799 3.775499 at 80iterations 0.1065073 2.022835 at 90iterations 6.0551949E-02 1.098263 at 100iterations 3.4546051E-02 0.6351395 at 110iterations 1.9715661E-02 0.3990860 at 120iterations 1.1219036E-02 0.2205182 at 130iterations 6.4043361E-03 0.1196232 at 140iterations 3.6471738E-03 7.6494694E-02 at 150iterations 2.0735476E-03 3.9283752E-02 at 160iterations 1.1841278E-03 2.1849632E-02 at 170iterations 6.7617500E-04 1.2445450E-02 at 180iterations finished qdiffx linear iterations at : 23:55:31 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 6.7617500E-04 1.2445450E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 23:55:31 12.839u 0.211s 0:13.33 97.8% 0+0k 0+0io 0pf+0w