Sat Oct 15 15:00:51 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 15 2011 at 15:00:51 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6094221 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): -10.44800 45.44300 ymin,ymax (A): 30.37000 88.78600 zmin,zma (A): -10.26500 45.56500 x,y,z range (A): 55.89100 58.41599 55.83000 scale (grids/A): 0.6094221 object centre (A): 17.49750 59.57800 17.65000 number of atom coordinates read : 2768 total number of charged atoms : 2629 net assigned charge : -0.4999894 assigned positive charge : 410.8746 centred at (gu) : 89.13795 89.48518 89.50533 assigned negative charge : -411.3758 centred at (gu) : 89.12936 89.46291 89.49176 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6949 nv = 96 ne = 84 npr = 55215 no. pairs analyzed = 55215 no. exposed pairs = 4112 no. arc points = 28989 no. surface atoms = 1348 nbur = 1420 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3258 m= 4 mr = 26 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 0.2000000 number of dielectric boundary points 4061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2848 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8548 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0900151E-09 3.7610537E-10 midg,1,midg; midg,igrid,midg -1.6012294E-09 7.7119383E-10 1,midg,midg; igrid,midg,midg -8.7186924E-10 1.3519351E-10 gauss-seidel spectral radius is 0.9860911 estimated iterations to convergence 69 setup time was (sec) 0.4200000 now iterating at: 15:00:52 rms-change max change #iterations 0.1166276 18.75911 at 10iterations 1.0287437E-02 1.480273 at 20iterations 9.6746202E-04 0.1418524 at 30iterations 1.4488352E-04 2.5262833E-02 at 40iterations 4.0944276E-05 8.8572502E-03 at 50iterations finished qdiffx linear iterations at : 15:00:55 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 4.0944276E-05 8.8572502E-03 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 15:00:56 3.828u 0.254s 0:04.53 89.8% 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 15 2011 at 15:00:56 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.828267 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): -10.44800 45.44300 ymin,ymax (A): 30.37000 88.78600 zmin,zma (A): -10.26500 45.56500 x,y,z range (A): 55.89100 58.41599 55.83000 scale (grids/A): 1.828267 object centre (A): 17.49750 59.57800 17.65000 number of atom coordinates read : 2768 total number of charged atoms : 2629 net assigned charge : -0.4999894 assigned positive charge : 410.8746 centred at (gu) : 87.41338 88.45489 88.51536 assigned negative charge : -411.3758 centred at (gu) : 87.38801 88.38867 88.47512 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 74474 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28989 grid for indexing accessible points = 1.400000 m= 24904 mr = 47414 m= 3655 mr = 16559 m= 171 mr = 1860 m= 4 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 37341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 149 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 20543 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) : 0.6094221 object centre at (A) : 17.49750 59.57800 17.65000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2342431E-03 -1.7303735E-02 midg,1,midg; midg,igrid,midg 1.2041178E-02 -6.1523728E-03 1,midg,midg; igrid,midg,midg 1.1244062E-02 3.6836707E-03 gauss-seidel spectral radius is 0.9985658 estimated iterations to convergence 209 setup time was (sec) 0.6600000 now iterating at: 15:00:57 rms-change max change #iterations 4.054303 159.5536 at 10iterations 1.847355 61.72002 at 20iterations 0.8434906 28.98155 at 30iterations 0.3873515 14.22631 at 40iterations 0.1775433 6.215221 at 50iterations 8.1063114E-02 2.451836 at 60iterations 3.7178364E-02 1.235156 at 70iterations 1.7065182E-02 0.5913143 at 80iterations 7.8573283E-03 0.2948017 at 90iterations 3.5960625E-03 0.1127472 at 100iterations 1.6634043E-03 5.3364515E-02 at 110iterations 7.7794510E-04 2.7846336E-02 at 120iterations finished qdiffx linear iterations at : 15:01:05 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 7.7794510E-04 2.7846336E-02 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.150000 DelPhi exited at 15:01:06 9.148u 0.282s 0:09.73 96.8% 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 15 2011 at 15:01:06 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2768 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.742400 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): -10.44800 45.44300 ymin,ymax (A): 30.37000 88.78600 zmin,zma (A): -10.26500 45.56500 x,y,z range (A): 55.89100 58.41599 55.83000 scale (grids/A): 2.742400 object centre (A): 17.49750 59.57800 17.65000 number of atom coordinates read : 2768 total number of charged atoms : 2629 net assigned charge : -0.4999894 assigned positive charge : 410.8746 centred at (gu) : 86.11996 87.68225 87.77293 assigned negative charge : -411.3758 centred at (gu) : 86.08202 87.58289 87.71268 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 172442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28989 grid for indexing accessible points = 1.400000 m= 80365 mr = 116637 m= 27429 mr = 61546 m= 6199 mr = 20314 m= 706 mr = 4059 m= 16 mr = 364 m= 0 mr = 2 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 84235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21030 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) : 1.828267 object centre at (A) : 17.49750 59.57800 17.65000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1220203 -0.1977139 midg,1,midg; midg,igrid,midg 0.3391714 -2.2655692E-02 1,midg,midg; igrid,midg,midg 0.2757147 7.6820841E-03 gauss-seidel spectral radius is 0.9992622 estimated iterations to convergence 291 setup time was (sec) 1.330000 now iterating at: 15:01:07 rms-change max change #iterations 9.948234 325.4727 at 10iterations 5.919985 162.3813 at 20iterations 3.487837 81.96558 at 30iterations 2.033588 46.30887 at 40iterations 1.187556 23.92153 at 50iterations 0.6903716 15.86160 at 60iterations 0.3998751 7.963388 at 70iterations 0.2309157 4.134842 at 80iterations 0.1337405 2.522346 at 90iterations 7.7344306E-02 1.505882 at 100iterations 4.4548612E-02 0.9209666 at 110iterations 2.5689105E-02 0.4609315 at 120iterations 1.4840245E-02 0.2699080 at 130iterations 8.5789524E-03 0.1702032 at 140iterations 4.9721100E-03 8.8323593E-02 at 150iterations 2.9149109E-03 5.5018425E-02 at 160iterations 1.7256956E-03 3.2966614E-02 at 170iterations 1.0487890E-03 2.1887779E-02 at 180iterations finished qdiffx linear iterations at : 15:01:21 total time elapsed so far: 15.09000 # loops : 180 mean,max change (kT/e) : 1.0487890E-03 2.1887779E-02 energy calculations done at 15.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.22000 DelPhi exited at 15:01:21 15.223u 0.300s 0:15.84 97.9% 0+0k 0+0io 0pf+0w