Sun Oct 16 14:13:38 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 Sun Oct 16 2011 at 14:13:38 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6427037 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): -2.065000 46.48000 ymin,ymax (A): -15.27500 30.06600 zmin,zma (A): -19.13400 36.25700 x,y,z range (A): 48.54500 45.34100 55.39100 scale (grids/A): 0.6427037 object centre (A): 22.20750 7.395500 8.561501 number of atom coordinates read : 2287 total number of charged atoms : 2219 net assigned charge : 4.806004 assigned positive charge : 342.6832 centred at (gu) : 90.30367 88.39425 90.10363 assigned negative charge : -337.8778 centred at (gu) : 90.36060 88.53252 90.10689 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6383 nv = 96 ne = 84 npr = 45909 no. pairs analyzed = 45909 no. exposed pairs = 2879 no. arc points = 20067 no. surface atoms = 987 nbur = 1300 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3496 m= 0 mr = 40 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.3000000 number of dielectric boundary points 3191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7763 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4956041E-09 7.0955726E-09 midg,1,midg; midg,igrid,midg 3.1318894E-08 -5.5624709E-09 1,midg,midg; igrid,midg,midg 1.2638334E-08 1.0975818E-09 gauss-seidel spectral radius is 0.9874305 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 14:13:39 rms-change max change #iterations 0.1383618 19.80198 at 10iterations 1.3809801E-02 2.041688 at 20iterations 1.4165778E-03 0.2578201 at 30iterations 1.7175234E-04 2.7966499E-02 at 40iterations 3.3581888E-05 5.9806537E-03 at 50iterations finished qdiffx linear iterations at : 14:13:42 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.3581888E-05 5.9806537E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:13:42 3.435u 0.145s 0:03.85 92.7% 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 Sun Oct 16 2011 at 14:13:42 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.928111 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): -2.065000 46.48000 ymin,ymax (A): -15.27500 30.06600 zmin,zma (A): -19.13400 36.25700 x,y,z range (A): 48.54500 45.34100 55.39100 scale (grids/A): 1.928111 object centre (A): 22.20750 7.395500 8.561501 number of atom coordinates read : 2287 total number of charged atoms : 2219 net assigned charge : 4.806004 assigned positive charge : 342.6832 centred at (gu) : 90.91063 85.18237 90.31029 assigned negative charge : -337.8778 centred at (gu) : 91.08180 85.59757 90.32053 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68915 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20067 grid for indexing accessible points = 1.400000 m= 24955 mr = 47743 m= 4197 mr = 18358 m= 240 mr = 2709 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1507 time to turn everything in is 0.5300000 number of dielectric boundary points 29428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17435 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) : 0.6427037 object centre at (A) : 22.20750 7.395500 8.561501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4118381E-02 1.2970011E-02 midg,1,midg; midg,igrid,midg 2.7359949E-02 -3.8789527E-03 1,midg,midg; igrid,midg,midg 4.7424575E-03 -3.5350569E-02 gauss-seidel spectral radius is 0.9986358 estimated iterations to convergence 215 setup time was (sec) 0.8300000 now iterating at: 14:13:43 rms-change max change #iterations 4.069636 195.3309 at 10iterations 1.899341 75.54115 at 20iterations 0.8923253 30.37305 at 30iterations 0.4201770 15.71386 at 40iterations 0.1968209 6.774814 at 50iterations 9.2193678E-02 3.076012 at 60iterations 4.3164708E-02 1.342528 at 70iterations 2.0287028E-02 0.6182709 at 80iterations 9.5471097E-03 0.3262501 at 90iterations 4.4601001E-03 0.1320515 at 100iterations 2.1008665E-03 7.2761536E-02 at 110iterations 9.8550715E-04 3.1320572E-02 at 120iterations finished qdiffx linear iterations at : 14:13:50 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 9.8550715E-04 3.1320572E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 14:13:51 7.844u 0.209s 0:08.34 96.4% 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 Sun Oct 16 2011 at 14:13:51 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2287 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.892167 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): -2.065000 46.48000 ymin,ymax (A): -15.27500 30.06600 zmin,zma (A): -19.13400 36.25700 x,y,z range (A): 48.54500 45.34100 55.39100 scale (grids/A): 2.892167 object centre (A): 22.20750 7.395500 8.561501 number of atom coordinates read : 2287 total number of charged atoms : 2219 net assigned charge : 4.806004 assigned positive charge : 342.6832 centred at (gu) : 91.36586 82.77345 90.46524 assigned negative charge : -337.8778 centred at (gu) : 91.62267 83.39648 90.48073 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 159734 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20067 grid for indexing accessible points = 1.400000 m= 80194 mr = 116294 m= 29946 mr = 65193 m= 7577 mr = 24066 m= 1083 mr = 5857 m= 72 mr = 684 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 5117 time to turn everything in is 1.350000 number of dielectric boundary points 66473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17751 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) : 1.928111 object centre at (A) : 22.20750 7.395500 8.561501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2325129 8.8449843E-02 midg,1,midg; midg,igrid,midg 0.2242444 -5.2342605E-02 1,midg,midg; igrid,midg,midg 4.7207270E-02 -0.4929101 gauss-seidel spectral radius is 0.9992572 estimated iterations to convergence 290 setup time was (sec) 1.670000 now iterating at: 14:13:53 rms-change max change #iterations 9.490979 396.6619 at 10iterations 5.562135 123.9427 at 20iterations 3.235003 72.86644 at 30iterations 1.884382 38.95582 at 40iterations 1.092503 21.64913 at 50iterations 0.6322072 13.41687 at 60iterations 0.3660363 7.511666 at 70iterations 0.2105508 3.839226 at 80iterations 0.1214989 2.353708 at 90iterations 7.0235148E-02 1.260584 at 100iterations 4.0373582E-02 0.7858152 at 110iterations 2.3236379E-02 0.4935913 at 120iterations 1.3346573E-02 0.2394361 at 130iterations 7.6743653E-03 0.1493340 at 140iterations 4.4124587E-03 8.2122803E-02 at 150iterations 2.5338936E-03 5.4774284E-02 at 160iterations 1.4578307E-03 3.0603409E-02 at 170iterations 8.3793432E-04 1.7052531E-02 at 180iterations finished qdiffx linear iterations at : 14:14:04 total time elapsed so far: 13.32000 # loops : 180 mean,max change (kT/e) : 8.3793432E-04 1.7052531E-02 energy calculations done at 13.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.51000 DelPhi exited at 14:14:05 13.516u 0.207s 0:14.01 97.8% 0+0k 0+0io 0pf+0w