Sat Oct 8 17:46:34 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 8 2011 at 17:46:35 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3506 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5233447 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): -0.8090000 45.13500 ymin,ymax (A): -30.51200 26.16300 zmin,zma (A): 1.359000 69.38300 x,y,z range (A): 45.94400 56.67500 68.02400 scale (grids/A): 0.5233447 object centre (A): 22.16300 -2.174500 35.37100 number of atom coordinates read : 3506 total number of charged atoms : 3359 net assigned charge : -5.871980 assigned positive charge : 537.6941 centred at (gu) : 90.36232 91.81684 90.56908 assigned negative charge : -543.5679 centred at (gu) : 90.32394 91.77336 90.56494 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6115 nv = 96 ne = 84 npr = 71538 no. pairs analyzed = 71538 no. exposed pairs = 4246 no. arc points = 28951 no. surface atoms = 1442 nbur = 2064 mkacc time = 0.1500000 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 = 1.624000 m= 192 mr = 3259 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3010 ## 447 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8178 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4047542E-10 -1.5478721E-10 midg,1,midg; midg,igrid,midg -1.8586883E-10 -6.0241021E-13 1,midg,midg; igrid,midg,midg -2.5273536E-10 -2.1687922E-11 gauss-seidel spectral radius is 0.9812261 estimated iterations to convergence 60 setup time was (sec) 0.5900000 now iterating at: 17:46:35 rms-change max change #iterations 6.6463932E-02 12.52655 at 10iterations 4.0796311E-03 0.7213497 at 20iterations 3.8517473E-04 6.6248417E-02 at 30iterations 8.4101754E-05 1.6890526E-02 at 40iterations 2.3105667E-05 4.4021606E-03 at 50iterations finished qdiffx linear iterations at : 17:46:38 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.3105667E-05 4.4021606E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:46:39 3.560u 0.228s 0:04.06 93.1% 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 8 2011 at 17:46:39 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3506 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.570034 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): -0.8090000 45.13500 ymin,ymax (A): -30.51200 26.16300 zmin,zma (A): 1.359000 69.38300 x,y,z range (A): 45.94400 56.67500 68.02400 scale (grids/A): 1.570034 object centre (A): 22.16300 -2.174500 35.37100 number of atom coordinates read : 3506 total number of charged atoms : 3359 net assigned charge : -5.871980 assigned positive charge : 537.6941 centred at (gu) : 91.08617 95.44964 91.70618 assigned negative charge : -543.5679 centred at (gu) : 90.97149 95.31973 91.69424 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68504 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20417 mr = 47673 m= 1789 mr = 13915 m= 26 mr = 747 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 85 time to turn everything in is 0.5000000 number of dielectric boundary points 28401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 429 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 25376 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) : 0.5233447 object centre at (A) : 22.16300 -2.174500 35.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9658487E-03 9.9649541E-03 midg,1,midg; midg,igrid,midg -7.7727940E-03 -1.1804031E-02 1,midg,midg; igrid,midg,midg -4.4831480E-03 1.1535344E-03 gauss-seidel spectral radius is 0.9980698 estimated iterations to convergence 181 setup time was (sec) 0.8200000 now iterating at: 17:46:40 rms-change max change #iterations 3.385560 148.5169 at 10iterations 1.377656 50.50020 at 20iterations 0.5589957 20.24493 at 30iterations 0.2274505 8.513718 at 40iterations 9.2325613E-02 3.265348 at 50iterations 3.7566345E-02 1.372314 at 60iterations 1.5281123E-02 0.5854938 at 70iterations 6.2670312E-03 0.2159348 at 80iterations 2.5790737E-03 9.7415924E-02 at 90iterations 1.0727878E-03 4.4816971E-02 at 100iterations 4.6478354E-04 1.7770767E-02 at 110iterations 2.1367848E-04 7.7428818E-03 at 120iterations finished qdiffx linear iterations at : 17:46:47 total time elapsed so far: 7.850000 # loops : 120 mean,max change (kT/e) : 2.1367848E-04 7.7428818E-03 energy calculations done at 7.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 17:46:47 8.030u 0.261s 0:08.71 95.1% 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 8 2011 at 17:46:47 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3506 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.355051 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): -0.8090000 45.13500 ymin,ymax (A): -30.51200 26.16300 zmin,zma (A): 1.359000 69.38300 x,y,z range (A): 45.94400 56.67500 68.02400 scale (grids/A): 2.355051 object centre (A): 22.16300 -2.174500 35.37100 number of atom coordinates read : 3506 total number of charged atoms : 3359 net assigned charge : -5.871980 assigned positive charge : 537.6941 centred at (gu) : 91.62886 98.17424 92.55911 assigned negative charge : -543.5679 centred at (gu) : 91.45710 97.97944 92.54131 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 159884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73113 mr = 117281 m= 18930 mr = 57794 m= 2548 mr = 13842 m= 122 mr = 1476 m= 0 mr = 27 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 332 time to turn everything in is 1.160000 number of dielectric boundary points 64177 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 26807 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) : 1.570034 object centre at (A) : 22.16300 -2.174500 35.37100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2030797 4.1150771E-02 midg,1,midg; midg,igrid,midg -0.1094740 -0.1620775 1,midg,midg; igrid,midg,midg -7.7788010E-02 3.7545834E-02 gauss-seidel spectral radius is 0.9991054 estimated iterations to convergence 264 setup time was (sec) 1.470000 now iterating at: 17:46:49 rms-change max change #iterations 9.008953 257.7068 at 10iterations 4.977938 132.6002 at 20iterations 2.748605 60.88177 at 30iterations 1.503882 32.43991 at 40iterations 0.8258621 17.50878 at 50iterations 0.4501776 10.80514 at 60iterations 0.2467632 4.955706 at 70iterations 0.1337460 3.040366 at 80iterations 7.2914109E-02 1.417275 at 90iterations 3.9624348E-02 0.8025723 at 100iterations 2.1635931E-02 0.4458899 at 110iterations 1.1808849E-02 0.2366028 at 120iterations 6.4275940E-03 0.1293982 at 130iterations 3.5157348E-03 7.7297211E-02 at 140iterations 1.9344672E-03 3.7521482E-02 at 150iterations 1.0738195E-03 2.4152756E-02 at 160iterations 6.0862151E-04 1.3195038E-02 at 170iterations 3.5523737E-04 7.7857971E-03 at 180iterations finished qdiffx linear iterations at : 17:47:00 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 3.5523737E-04 7.7857971E-03 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 17:47:01 12.795u 0.309s 0:13.37 97.9% 0+0k 0+0io 0pf+0w