Sat Oct 15 11:29:45 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 11:29:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4288 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5428981 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): -0.6120000 64.96200 ymin,ymax (A): -25.33800 36.67700 zmin,zma (A): -23.39900 32.53800 x,y,z range (A): 65.57400 62.01500 55.93700 scale (grids/A): 0.5428981 object centre (A): 32.17500 5.669501 4.569499 number of atom coordinates read : 4288 total number of charged atoms : 4131 net assigned charge : -9.499973 assigned positive charge : 652.4443 centred at (gu) : 88.90652 89.18217 90.90733 assigned negative charge : -661.9485 centred at (gu) : 88.97701 89.19427 90.87097 start vw surface at 0.2500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 8243 nv = 96 ne = 84 npr = 83845 no. pairs analyzed = 83845 no. exposed pairs = 5898 no. arc points = 40741 no. surface atoms = 1961 nbur = 2327 mkacc time = 0.2500000 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 = 1.596000 m= 355 mr = 4110 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4007 ## 527 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 10879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8503769E-10 -2.6524419E-10 midg,1,midg; midg,igrid,midg -5.2081756E-10 -5.2554627E-10 1,midg,midg; igrid,midg,midg 1.1435942E-10 -8.8567409E-10 gauss-seidel spectral radius is 0.9826162 estimated iterations to convergence 62 setup time was (sec) 0.8400000 now iterating at: 11:29:46 rms-change max change #iterations 8.8662408E-02 13.57091 at 10iterations 6.1727040E-03 0.8640575 at 20iterations 7.4920797E-04 0.1135900 at 30iterations 2.0851054E-04 3.0807495E-02 at 40iterations 6.7236506E-05 9.7818375E-03 at 50iterations finished qdiffx linear iterations at : 11:29:50 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 6.7236506E-05 9.7818375E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 11:29:50 4.531u 0.230s 0:05.12 92.9% 0+0k 0+0io 6pf+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 11:29:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4288 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.628694 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): -0.6120000 64.96200 ymin,ymax (A): -25.33800 36.67700 zmin,zma (A): -23.39900 32.53800 x,y,z range (A): 65.57400 62.01500 55.93700 scale (grids/A): 1.628694 object centre (A): 32.17500 5.669501 4.569499 number of atom coordinates read : 4288 total number of charged atoms : 4131 net assigned charge : -9.499973 assigned positive charge : 652.4443 centred at (gu) : 86.71786 87.54508 92.72039 assigned negative charge : -661.9485 centred at (gu) : 86.93066 87.58257 92.61249 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 91406 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40741 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 28739 mr = 60989 m= 3005 mr = 18888 m= 80 mr = 1330 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 42014 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 479 ## 2 charges are in solution ## iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 31577 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) : 0.5428981 object centre at (A) : 32.17500 5.669501 4.569499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4175232E-02 -1.3623728E-03 midg,1,midg; midg,igrid,midg -1.1733719E-02 -1.5904231E-03 1,midg,midg; igrid,midg,midg -7.9410922E-05 -2.0236511E-02 gauss-seidel spectral radius is 0.9983217 estimated iterations to convergence 194 setup time was (sec) 1.240000 now iterating at: 11:29:52 rms-change max change #iterations 4.149590 161.0370 at 10iterations 1.780143 62.77872 at 20iterations 0.7655104 26.05475 at 30iterations 0.3298418 11.87224 at 40iterations 0.1418230 5.108600 at 50iterations 6.1358843E-02 1.887190 at 60iterations 2.6445851E-02 0.8613291 at 70iterations 1.1471870E-02 0.3794022 at 80iterations 4.9963766E-03 0.1516514 at 90iterations 2.1976132E-03 7.1456909E-02 at 100iterations 9.8883652E-04 3.4194946E-02 at 110iterations 4.6473008E-04 1.4282227E-02 at 120iterations finished qdiffx linear iterations at : 11:30:01 total time elapsed so far: 10.19000 # loops : 120 mean,max change (kT/e) : 4.6473008E-04 1.4282227E-02 energy calculations done at 10.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.42000 DelPhi exited at 11:30:01 10.422u 0.289s 0:11.16 95.8% 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 11:30:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4288 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.443042 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): -0.6120000 64.96200 ymin,ymax (A): -25.33800 36.67700 zmin,zma (A): -23.39900 32.53800 x,y,z range (A): 65.57400 62.01500 55.93700 scale (grids/A): 2.443042 object centre (A): 32.17500 5.669501 4.569499 number of atom coordinates read : 4288 total number of charged atoms : 4131 net assigned charge : -9.499973 assigned positive charge : 652.4443 centred at (gu) : 85.07655 86.31726 94.08031 assigned negative charge : -661.9485 centred at (gu) : 85.39595 86.37362 93.91863 start vw surface at 0.2300000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 211974 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40741 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 98599 mr = 149880 m= 28173 mr = 75886 m= 4522 mr = 20290 m= 353 mr = 2750 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.100000 number of dielectric boundary points 94696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 32998 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) : 1.628694 object centre at (A) : 32.17500 5.669501 4.569499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1292663 3.9021645E-02 midg,1,midg; midg,igrid,midg -0.1927922 7.0424981E-02 1,midg,midg; igrid,midg,midg 3.8760994E-03 -0.5132493 gauss-seidel spectral radius is 0.9992248 estimated iterations to convergence 284 setup time was (sec) 2.500000 now iterating at: 11:30:04 rms-change max change #iterations 11.03368 325.8927 at 10iterations 6.540740 168.4228 at 20iterations 3.838917 97.33739 at 30iterations 2.235074 52.59211 at 40iterations 1.294806 27.53384 at 50iterations 0.7464573 15.75998 at 60iterations 0.4284389 8.479239 at 70iterations 0.2456423 6.125139 at 80iterations 0.1404265 2.696999 at 90iterations 8.0164269E-02 1.732128 at 100iterations 4.5764931E-02 0.8023176 at 110iterations 2.6102072E-02 0.4792328 at 120iterations 1.4848473E-02 0.3005371 at 130iterations 8.4561938E-03 0.1756063 at 140iterations 4.8180227E-03 8.4304810E-02 at 150iterations 2.7544813E-03 4.9097776E-02 at 160iterations 1.5763830E-03 3.1509399E-02 at 170iterations 9.0872077E-04 1.6803741E-02 at 180iterations finished qdiffx linear iterations at : 11:30:19 total time elapsed so far: 17.10000 # loops : 180 mean,max change (kT/e) : 9.0872077E-04 1.6803741E-02 energy calculations done at 17.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.34000 DelPhi exited at 11:30:19 17.344u 0.280s 0:18.06 97.5% 0+0k 0+0io 0pf+0w