Tue Oct 11 06:00:14 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 06:00:14 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 # of charge parameter records: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7078801 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): 25.84200 72.30800 ymin,ymax (A): -18.70400 31.58700 zmin,zma (A): 4.210000 46.47600 x,y,z range (A): 46.46600 50.29100 42.26600 scale (grids/A): 0.7078801 object centre (A): 49.07500 6.441500 25.34300 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.24303 90.18902 90.24995 assigned negative charge : -318.8441 centred at (gu) : 89.37321 90.13958 90.33080 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7250 nv = 96 ne = 84 npr = 42319 no. pairs analyzed = 42319 no. exposed pairs = 2601 no. arc points = 17669 no. surface atoms = 893 nbur = 1434 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4197 m= 1 mr = 102 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 0.2600000 number of dielectric boundary points 3438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1636 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1389531E-08 1.3883533E-08 midg,1,midg; midg,igrid,midg 2.8635178E-08 8.3023238E-08 1,midg,midg; igrid,midg,midg 1.3972065E-07 -1.0181079E-08 gauss-seidel spectral radius is 0.9896015 estimated iterations to convergence 80 setup time was (sec) 0.4700000 now iterating at: 06:00:15 rms-change max change #iterations 0.2018012 38.18176 at 10iterations 2.5257925E-02 3.563931 at 20iterations 3.3339360E-03 0.4372387 at 30iterations 5.7751441E-04 7.7465057E-02 at 40iterations 1.5520748E-04 2.0330429E-02 at 50iterations finished qdiffx linear iterations at : 06:00:17 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 1.5520748E-04 2.0330429E-02 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 06:00:18 3.079u 0.152s 0:03.67 87.7% 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 Tue Oct 11 2011 at 06:00:18 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 = 2327 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: 2.123640 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): 25.84200 72.30800 ymin,ymax (A): -18.70400 31.58700 zmin,zma (A): 4.210000 46.47600 x,y,z range (A): 46.46600 50.29100 42.26600 scale (grids/A): 2.123640 object centre (A): 49.07500 6.441500 25.34300 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.72904 90.56716 90.74963 assigned negative charge : -318.8441 centred at (gu) : 88.11976 90.41875 90.99243 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76855 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17669 grid for indexing accessible points = 1.400000 m= 31490 mr = 54807 m= 6194 mr = 24121 m= 597 mr = 4211 m= 20 mr = 322 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 31693 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15885 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) : 0.7078801 object centre at (A) : 49.07500 6.441500 25.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1079395E-02 2.8597595E-02 midg,1,midg; midg,igrid,midg 4.6168309E-02 2.4314592E-02 1,midg,midg; igrid,midg,midg 4.5367260E-02 -4.7639955E-02 gauss-seidel spectral radius is 0.9988379 estimated iterations to convergence 232 setup time was (sec) 0.8900000 now iterating at: 06:00:19 rms-change max change #iterations 4.656786 169.2372 at 10iterations 2.308309 76.35873 at 20iterations 1.147606 38.92577 at 30iterations 0.5711894 17.06184 at 40iterations 0.2847172 8.342816 at 50iterations 0.1416791 4.314476 at 60iterations 7.0427552E-02 2.080023 at 70iterations 3.5181332E-02 1.113892 at 80iterations 1.7541489E-02 0.5288966 at 90iterations 8.8068731E-03 0.2495508 at 100iterations 4.4532078E-03 0.1239367 at 110iterations 2.3050124E-03 6.9282532E-02 at 120iterations finished qdiffx linear iterations at : 06:00:25 total time elapsed so far: 7.340000 # loops : 120 mean,max change (kT/e) : 2.3050124E-03 6.9282532E-02 energy calculations done at 7.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 06:00:26 7.513u 0.211s 0:08.25 93.5% 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 06:00:26 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 = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.185461 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): 25.84200 72.30800 ymin,ymax (A): -18.70400 31.58700 zmin,zma (A): 4.210000 46.47600 x,y,z range (A): 46.46600 50.29100 42.26600 scale (grids/A): 3.185461 object centre (A): 49.07500 6.441500 25.34300 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.59354 90.85058 91.12452 assigned negative charge : -318.8441 centred at (gu) : 87.17967 90.62819 91.48877 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 177266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17669 grid for indexing accessible points = 1.400000 m= 97708 mr = 132093 m= 40155 mr = 81568 m= 11842 mr = 33274 m= 2501 mr = 9320 m= 293 mr = 1858 m= 18 mr = 197 m= 0 mr = 2 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.810000 number of dielectric boundary points 71471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 16016 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) : 2.123640 object centre at (A) : 49.07500 6.441500 25.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1171087 0.2398417 midg,1,midg; midg,igrid,midg 0.3835068 0.1176765 1,midg,midg; igrid,midg,midg 0.4308622 -0.6057129 gauss-seidel spectral radius is 0.9992989 estimated iterations to convergence 298 setup time was (sec) 2.120000 now iterating at: 06:00:29 rms-change max change #iterations 10.36094 354.8170 at 10iterations 6.142180 132.9464 at 20iterations 3.637517 78.70394 at 30iterations 2.148387 45.97802 at 40iterations 1.265524 27.06361 at 50iterations 0.7449456 14.25580 at 60iterations 0.4378466 8.215769 at 70iterations 0.2576191 4.531578 at 80iterations 0.1511246 2.646190 at 90iterations 8.8733792E-02 1.602668 at 100iterations 5.2181017E-02 0.9085445 at 110iterations 3.0718394E-02 0.5393143 at 120iterations 1.8197808E-02 0.3107309 at 130iterations 1.0913393E-02 0.1978674 at 140iterations 6.6934698E-03 0.1155396 at 150iterations 4.2292350E-03 7.5336456E-02 at 160iterations 2.8226399E-03 5.0827026E-02 at 170iterations 2.0036895E-03 3.4790039E-02 at 180iterations finished qdiffx linear iterations at : 06:00:39 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 2.0036895E-03 3.4790039E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.45000 DelPhi exited at 06:00:39 12.457u 0.229s 0:13.26 95.5% 0+0k 0+0io 0pf+0w