Sat Oct 15 12:00:34 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 Sat Oct 15 2011 at 12:00:34 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: HIT 84 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: 0.5891600 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): 42.10700 102.5320 ymin,ymax (A): 37.39000 81.58900 zmin,zma (A): -13.87600 40.61200 x,y,z range (A): 60.42501 44.19900 54.48800 scale (grids/A): 0.5891600 object centre (A): 72.31950 59.48950 13.36800 number of atom coordinates read : 2490 total number of charged atoms : 2353 net assigned charge : 9.514032 assigned positive charge : 364.7241 centred at (gu) : 89.84322 89.70193 89.56577 assigned negative charge : -355.2108 centred at (gu) : 89.86825 89.80058 89.62978 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5765 nv = 96 ne = 84 npr = 49841 no. pairs analyzed = 49841 no. exposed pairs = 3322 no. arc points = 23954 no. surface atoms = 1111 nbur = 1379 mkacc time = 0.1400000 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 = 1.484000 m= 263 mr = 2859 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.2900000 number of dielectric boundary points 3150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2424 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7344 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7914055E-09 1.1881712E-09 midg,1,midg; midg,igrid,midg 5.5103695E-09 4.4055715E-10 1,midg,midg; igrid,midg,midg 3.5474832E-09 2.1600064E-09 gauss-seidel spectral radius is 0.9850940 estimated iterations to convergence 67 setup time was (sec) 0.5900000 now iterating at: 12:00:35 rms-change max change #iterations 9.6626453E-02 15.04435 at 10iterations 7.8656962E-03 1.243961 at 20iterations 6.5603707E-04 0.1077118 at 30iterations 6.5793749E-05 1.0982513E-02 at 40iterations 9.9016461E-06 1.9454956E-03 at 50iterations finished qdiffx linear iterations at : 12:00:40 total time elapsed so far: 5.040000 # loops : 50 mean,max change (kT/e) : 9.9016461E-06 1.9454956E-03 energy calculations done at 5.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.220000 DelPhi exited at 12:00:40 5.226u 0.470s 0:06.02 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 Sat Oct 15 2011 at 12:00:40 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: HIT 84 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: 1.767480 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): 42.10700 102.5320 ymin,ymax (A): 37.39000 81.58900 zmin,zma (A): -13.87600 40.61200 x,y,z range (A): 60.42501 44.19900 54.48800 scale (grids/A): 1.767480 object centre (A): 72.31950 59.48950 13.36800 number of atom coordinates read : 2490 total number of charged atoms : 2353 net assigned charge : 9.514032 assigned positive charge : 364.7241 centred at (gu) : 89.52925 89.10523 88.69665 assigned negative charge : -355.2108 centred at (gu) : 89.60454 89.40172 88.88928 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 20224 mr = 41068 m= 2774 mr = 13691 m= 122 mr = 1525 m= 0 mr = 26 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 577 time to turn everything in is 0.5200000 number of dielectric boundary points 29418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18332 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) : 0.5891600 object centre at (A) : 72.31950 59.48950 13.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8578987E-02 1.3552250E-02 midg,1,midg; midg,igrid,midg 1.6315535E-02 -5.0166822E-03 1,midg,midg; igrid,midg,midg 1.8519873E-02 3.3970129E-02 gauss-seidel spectral radius is 0.9984185 estimated iterations to convergence 200 setup time was (sec) 0.8500000 now iterating at: 12:00:42 rms-change max change #iterations 3.479175 175.9213 at 10iterations 1.531816 58.75251 at 20iterations 0.6740474 24.11519 at 30iterations 0.2982970 10.89872 at 40iterations 0.1318149 4.483353 at 50iterations 5.7837822E-02 2.342236 at 60iterations 2.5594499E-02 0.9242172 at 70iterations 1.1299305E-02 0.3749847 at 80iterations 4.9921582E-03 0.1744747 at 90iterations 2.2030878E-03 7.8710735E-02 at 100iterations 9.7638182E-04 3.8965225E-02 at 110iterations 4.3241144E-04 1.5090942E-02 at 120iterations finished qdiffx linear iterations at : 12:00:53 total time elapsed so far: 12.16000 # loops : 120 mean,max change (kT/e) : 4.3241144E-04 1.5090942E-02 energy calculations done at 12.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 12:00:54 12.319u 0.574s 0:13.26 97.1% 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 15 2011 at 12:00:54 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2490 !!! WARNING: HIT 84 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: 2.651220 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): 42.10700 102.5320 ymin,ymax (A): 37.39000 81.58900 zmin,zma (A): -13.87600 40.61200 x,y,z range (A): 60.42501 44.19900 54.48800 scale (grids/A): 2.651220 object centre (A): 72.31950 59.48950 13.36800 number of atom coordinates read : 2490 total number of charged atoms : 2353 net assigned charge : 9.514032 assigned positive charge : 364.7241 centred at (gu) : 89.29381 88.65775 88.04496 assigned negative charge : -355.2108 centred at (gu) : 89.40678 89.10258 88.33384 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 145100 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23954 grid for indexing accessible points = 1.400000 m= 67057 mr = 100582 m= 21891 mr = 52311 m= 4638 mr = 16507 m= 547 mr = 3192 m= 19 mr = 327 m= 0 mr = 0 time to grow re-entrant surface = 0.8099999 no. cavity mid-points inaccessible to solvent = 1962 time to turn everything in is 1.350000 number of dielectric boundary points 66333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 18820 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) : 1.767480 object centre at (A) : 72.31950 59.48950 13.36800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3231363 0.1764510 midg,1,midg; midg,igrid,midg 0.1999530 -8.6627252E-02 1,midg,midg; igrid,midg,midg 0.3980382 0.5343093 gauss-seidel spectral radius is 0.9992065 estimated iterations to convergence 280 setup time was (sec) 1.750000 now iterating at: 12:00:56 rms-change max change #iterations 8.718537 316.3079 at 10iterations 5.053264 157.7810 at 20iterations 2.898707 66.13492 at 30iterations 1.653297 43.00839 at 40iterations 0.9403361 21.94402 at 50iterations 0.5342220 11.81954 at 60iterations 0.3026661 6.374379 at 70iterations 0.1709516 4.069524 at 80iterations 9.6631646E-02 1.939583 at 90iterations 5.4503743E-02 1.148979 at 100iterations 3.0877138E-02 0.6079092 at 110iterations 1.7392736E-02 0.3719659 at 120iterations 9.8164696E-03 0.2097206 at 130iterations 5.5362685E-03 0.1077900 at 140iterations 3.1172920E-03 6.9667667E-02 at 150iterations 1.7511726E-03 3.6418915E-02 at 160iterations 9.8777970E-04 1.9191742E-02 at 170iterations 5.5664754E-04 1.1367798E-02 at 180iterations finished qdiffx linear iterations at : 12:01:16 total time elapsed so far: 21.68000 # loops : 180 mean,max change (kT/e) : 5.5664754E-04 1.1367798E-02 energy calculations done at 21.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.85000 DelPhi exited at 12:01:16 21.854u 0.562s 0:22.81 98.2% 0+0k 0+0io 0pf+0w