Tue Oct 11 06:00:47 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 Tue Oct 11 2011 at 06:00:47 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7060130 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): 25.68500 72.99700 ymin,ymax (A): -18.74800 31.67600 zmin,zma (A): 3.821000 46.19600 x,y,z range (A): 47.31200 50.42400 42.37500 scale (grids/A): 0.7060130 object centre (A): 49.34100 6.464001 25.00850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 88.89204 90.15389 90.35725 assigned negative charge : -317.2741 centred at (gu) : 89.01663 90.11005 90.44029 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7131 nv = 96 ne = 84 npr = 42571 no. pairs analyzed = 42571 no. exposed pairs = 2570 no. arc points = 17322 no. surface atoms = 876 nbur = 1442 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4107 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1612 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7909 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6324086E-08 1.2260530E-08 midg,1,midg; midg,igrid,midg 3.0121406E-08 7.5843445E-08 1,midg,midg; igrid,midg,midg 1.3948639E-07 -6.6584773E-09 gauss-seidel spectral radius is 0.9895449 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:00:48 rms-change max change #iterations 0.2025961 27.95064 at 10iterations 2.4844063E-02 3.399872 at 20iterations 3.3286938E-03 0.5975647 at 30iterations 5.5677129E-04 7.1512222E-02 at 40iterations 1.4236060E-04 1.7755032E-02 at 50iterations finished qdiffx linear iterations at : 06:00:51 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.4236060E-04 1.7755032E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:00:51 3.402u 0.173s 0:04.17 85.6% 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 Tue Oct 11 2011 at 06:00:51 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.118039 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): 25.68500 72.99700 ymin,ymax (A): -18.74800 31.67600 zmin,zma (A): 3.821000 46.19600 x,y,z range (A): 47.31200 50.42400 42.37500 scale (grids/A): 2.118039 object centre (A): 49.34100 6.464001 25.00850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 86.67593 90.46161 91.07191 assigned negative charge : -317.2741 centred at (gu) : 87.04987 90.33006 91.32104 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 75819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17322 grid for indexing accessible points = 1.400000 m= 30903 mr = 54179 m= 5865 mr = 23564 m= 547 mr = 3912 m= 18 mr = 270 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 31227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15809 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) : 0.7060130 object centre at (A) : 49.34100 6.464001 25.00850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1024916E-02 2.8192133E-02 midg,1,midg; midg,igrid,midg 4.9197327E-02 2.7643114E-02 1,midg,midg; igrid,midg,midg 4.5274328E-02 -3.8546961E-02 gauss-seidel spectral radius is 0.9988286 estimated iterations to convergence 231 setup time was (sec) 0.6300000 now iterating at: 06:00:52 rms-change max change #iterations 4.602356 175.8891 at 10iterations 2.277485 79.63041 at 20iterations 1.131323 34.34499 at 30iterations 0.5601528 17.93831 at 40iterations 0.2775692 8.384634 at 50iterations 0.1380350 4.183098 at 60iterations 6.8511054E-02 1.990570 at 70iterations 3.4102842E-02 1.052448 at 80iterations 1.6953446E-02 0.5624971 at 90iterations 8.4813470E-03 0.2496357 at 100iterations 4.2708549E-03 0.1316509 at 110iterations 2.1789309E-03 7.2096825E-02 at 120iterations finished qdiffx linear iterations at : 06:00:59 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.1789309E-03 7.2096825E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 06:01:00 7.933u 0.178s 0:08.57 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 Tue Oct 11 2011 at 06:01:00 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.177058 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): 25.68500 72.99700 ymin,ymax (A): -18.74800 31.67600 zmin,zma (A): 3.821000 46.19600 x,y,z range (A): 47.31200 50.42400 42.37500 scale (grids/A): 3.177058 object centre (A): 49.34100 6.464001 25.00850 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 85.01380 90.69242 91.60785 assigned negative charge : -317.2741 centred at (gu) : 85.57481 90.49512 91.98151 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 175060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17322 grid for indexing accessible points = 1.400000 m= 96025 mr = 130639 m= 39093 mr = 80150 m= 11092 mr = 32311 m= 2216 mr = 8573 m= 270 mr = 1565 m= 19 mr = 185 m= 0 mr = 5 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 70347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 15951 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) : 2.118039 object centre at (A) : 49.34100 6.464001 25.00850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1232738 0.2379916 midg,1,midg; midg,igrid,midg 0.4355687 0.1221109 1,midg,midg; igrid,midg,midg 0.4677820 -0.4496109 gauss-seidel spectral radius is 0.9992971 estimated iterations to convergence 298 setup time was (sec) 1.380000 now iterating at: 06:01:02 rms-change max change #iterations 10.27555 395.1503 at 10iterations 6.093865 173.9972 at 20iterations 3.606851 82.73087 at 30iterations 2.124601 42.61200 at 40iterations 1.249890 23.61193 at 50iterations 0.7370163 15.08000 at 60iterations 0.4323752 7.475388 at 70iterations 0.2531972 4.276452 at 80iterations 0.1487061 2.528625 at 90iterations 8.7132163E-02 1.762783 at 100iterations 5.1306177E-02 0.8433361 at 110iterations 3.0144669E-02 0.4958634 at 120iterations 1.7850939E-02 0.3110504 at 130iterations 1.0679049E-02 0.1777916 at 140iterations 6.5161875E-03 0.1300855 at 150iterations 4.0769246E-03 7.1388245E-02 at 160iterations 2.6879555E-03 5.2219391E-02 at 170iterations 1.8725803E-03 3.4145355E-02 at 180iterations finished qdiffx linear iterations at : 06:01:13 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 1.8725803E-03 3.4145355E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 06:01:13 12.606u 0.218s 0:13.17 97.2% 0+0k 0+0io 0pf+0w