Wed Feb 15 08:55:09 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:10 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 0.6411065 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 0.6411065 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2726 total number of charged atoms : 2578 net assigned charge : -0.4999861 assigned positive charge : 412.2798 centred at (gu) : 90.13236 90.36057 91.81730 assigned negative charge : -412.7803 centred at (gu) : 89.90725 90.23335 91.72100 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7321 nv = 96 ne = 84 npr = 57206 no. pairs analyzed = 57206 no. exposed pairs = 3362 no. arc points = 23299 no. surface atoms = 1126 nbur = 1600 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 4090 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3200000 number of dielectric boundary points 3605 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2306 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8986 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1064676E-09 1.6582058E-08 midg,1,midg; midg,igrid,midg -1.6180204E-08 1.6167320E-08 1,midg,midg; igrid,midg,midg -2.9601942E-08 2.7740954E-08 gauss-seidel spectral radius is 0.9874005 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 08:55:10 rms-change max change #iterations 0.1534113 22.18402 at 10iterations 1.5535808E-02 2.086637 at 20iterations 1.5774081E-03 0.2256594 at 30iterations 1.6183301E-04 2.0309448E-02 at 40iterations 1.7376824E-05 2.6865005E-03 at 50iterations finished qdiffx linear iterations at : 08:55:13 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.7376824E-05 2.6865005E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 08:55:14 3.575u 0.170s 0:04.36 85.7% 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 Wed Feb 15 2012 at 08:55:14 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.923319 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 1.923319 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2726 total number of charged atoms : 2578 net assigned charge : -0.4999861 assigned positive charge : 412.2798 centred at (gu) : 90.39651 91.08105 95.45107 assigned negative charge : -412.7803 centred at (gu) : 89.72146 90.69980 95.16262 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 79700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23299 grid for indexing accessible points = 1.400000 m= 28929 mr = 56012 m= 4367 mr = 21397 m= 242 mr = 2686 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.6300000 number of dielectric boundary points 33068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20297 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) : 0.6411065 object centre at (A) : 12.83000 -1.701000 17.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7069918E-02 -6.0610441E-03 midg,1,midg; midg,igrid,midg -1.4060159E-02 2.1046920E-02 1,midg,midg; igrid,midg,midg -1.1721280E-02 4.4161648E-02 gauss-seidel spectral radius is 0.9986705 estimated iterations to convergence 217 setup time was (sec) 0.9000000 now iterating at: 08:55:15 rms-change max change #iterations 4.520636 193.3732 at 10iterations 2.145984 70.55748 at 20iterations 1.018880 33.71189 at 30iterations 0.4825920 15.09154 at 40iterations 0.2285758 7.517536 at 50iterations 0.1082144 3.756962 at 60iterations 5.1245414E-02 1.487000 at 70iterations 2.4297768E-02 0.7272072 at 80iterations 1.1523933E-02 0.3425140 at 90iterations 5.4572742E-03 0.1691628 at 100iterations 2.5873836E-03 9.1798782E-02 at 110iterations 1.2349521E-03 3.9583206E-02 at 120iterations finished qdiffx linear iterations at : 08:55:22 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.2349521E-03 3.9583206E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 08:55:22 7.493u 0.185s 0:08.16 93.9% 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 Wed Feb 15 2012 at 08:55:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 944 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 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: 2.884979 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): -11.37100 37.03100 ymin,ymax (A): -25.82100 22.41900 zmin,zma (A): -10.26600 45.26300 x,y,z range (A): 48.40200 48.24000 55.52900 scale (grids/A): 2.884979 object centre (A): 12.83000 -1.701000 17.49850 number of atom coordinates read : 2726 total number of charged atoms : 2578 net assigned charge : -0.4999861 assigned positive charge : 412.2798 centred at (gu) : 90.59458 91.62148 98.17642 assigned negative charge : -412.7803 centred at (gu) : 89.58227 91.04969 97.74394 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 184467 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23299 grid for indexing accessible points = 1.400000 m= 93996 mr = 135835 m= 33576 mr = 77118 m= 7946 mr = 26868 m= 1141 mr = 5938 m= 57 mr = 796 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 1856 time to turn everything in is 1.450000 number of dielectric boundary points 74611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 20624 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) : 1.923319 object centre at (A) : 12.83000 -1.701000 17.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6056429 0.1860069 midg,1,midg; midg,igrid,midg -0.1559980 0.2574102 1,midg,midg; igrid,midg,midg -7.1381263E-02 0.3727978 gauss-seidel spectral radius is 0.9992675 estimated iterations to convergence 292 setup time was (sec) 1.740000 now iterating at: 08:55:27 rms-change max change #iterations 10.57833 462.8671 at 10iterations 6.200170 132.3691 at 20iterations 3.632154 79.85428 at 30iterations 2.120625 54.90937 at 40iterations 1.233340 25.75929 at 50iterations 0.7162669 14.23868 at 60iterations 0.4145923 7.445739 at 70iterations 0.2406696 4.232109 at 80iterations 0.1387909 2.502085 at 90iterations 8.0458865E-02 1.541884 at 100iterations 4.6504207E-02 0.8348694 at 110iterations 2.6870748E-02 0.4811441 at 120iterations 1.5521322E-02 0.2932181 at 130iterations 8.9655584E-03 0.1623363 at 140iterations 5.1895520E-03 8.8985443E-02 at 150iterations 3.0025411E-03 5.1922798E-02 at 160iterations 1.7356754E-03 3.5570145E-02 at 170iterations 1.0076282E-03 1.8901825E-02 at 180iterations finished qdiffx linear iterations at : 08:55:37 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 1.0076282E-03 1.8901825E-02 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 08:55:37 11.974u 0.255s 0:12.63 96.7% 0+0k 0+0io 0pf+0w