Mon Oct 10 12:12:37 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 Mon Oct 10 2011 at 12:12:37 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7416975 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): 8.332001 56.33000 ymin,ymax (A): -9.149000 36.52500 zmin,zma (A): -2.976000 44.17600 x,y,z range (A): 47.99800 45.67400 47.15200 scale (grids/A): 0.7416975 object centre (A): 32.33100 13.68800 20.60000 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.50508 90.51048 89.85905 assigned negative charge : -323.3720 centred at (gu) : 89.51368 90.60142 90.03532 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8038 nv = 96 ne = 84 npr = 43059 no. pairs analyzed = 43059 no. exposed pairs = 2738 no. arc points = 19223 no. surface atoms = 932 nbur = 1185 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 578 mr = 4461 m= 3 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1611 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.2033046E-08 -2.9677074E-07 midg,1,midg; midg,igrid,midg -1.7354802E-08 -2.3275871E-07 1,midg,midg; igrid,midg,midg -1.1484386E-07 -1.1285204E-07 gauss-seidel spectral radius is 0.9905291 estimated iterations to convergence 83 setup time was (sec) 0.5400000 now iterating at: 12:12:38 rms-change max change #iterations 0.2464873 34.52714 at 10iterations 3.3933070E-02 4.045605 at 20iterations 4.5669465E-03 0.5653868 at 30iterations 6.1943149E-04 8.5813522E-02 at 40iterations 8.2670995E-05 1.0433197E-02 at 50iterations finished qdiffx linear iterations at : 12:12:42 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 8.2670995E-05 1.0433197E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 12:12:43 4.401u 0.406s 0:05.17 92.8% 0+0k 0+0io 4pf+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 Mon Oct 10 2011 at 12:12:43 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.225093 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): 8.332001 56.33000 ymin,ymax (A): -9.149000 36.52500 zmin,zma (A): -2.976000 44.17600 x,y,z range (A): 47.99800 45.67400 47.15200 scale (grids/A): 2.225093 object centre (A): 32.33100 13.68800 20.60000 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.51532 91.53135 89.57723 assigned negative charge : -323.3720 centred at (gu) : 88.54134 91.80424 90.10581 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 34017 mr = 58110 m= 7202 mr = 25962 m= 753 mr = 4955 m= 19 mr = 393 m= 0 mr = 3 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 37141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15769 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) : 0.7416975 object centre at (A) : 32.33100 13.68800 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6329818E-03 -0.1174260 midg,1,midg; midg,igrid,midg -3.0066773E-02 -5.3832360E-02 1,midg,midg; igrid,midg,midg -6.4341733E-03 5.6265527E-03 gauss-seidel spectral radius is 0.9989323 estimated iterations to convergence 242 setup time was (sec) 1.000000 now iterating at: 12:12:44 rms-change max change #iterations 5.109219 206.8746 at 10iterations 2.595914 79.58600 at 20iterations 1.322883 38.59495 at 30iterations 0.6765456 18.80528 at 40iterations 0.3460118 10.19610 at 50iterations 0.1768231 5.913742 at 60iterations 9.0321817E-02 2.787137 at 70iterations 4.6160266E-02 1.307045 at 80iterations 2.3556883E-02 0.6748929 at 90iterations 1.2069764E-02 0.3384495 at 100iterations 6.1646244E-03 0.1844702 at 110iterations 3.1516198E-03 8.6925507E-02 at 120iterations finished qdiffx linear iterations at : 12:12:54 total time elapsed so far: 10.49000 # loops : 120 mean,max change (kT/e) : 3.1516198E-03 8.6925507E-02 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.65000 DelPhi exited at 12:12:54 10.658u 0.446s 0:11.72 94.6% 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 Mon Oct 10 2011 at 12:12:54 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.337639 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): 8.332001 56.33000 ymin,ymax (A): -9.149000 36.52500 zmin,zma (A): -2.976000 44.17600 x,y,z range (A): 47.99800 45.67400 47.15200 scale (grids/A): 3.337639 object centre (A): 32.33100 13.68800 20.60000 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.77296 92.29688 89.36591 assigned negative charge : -323.3720 centred at (gu) : 87.81204 92.70649 90.15880 start vw surface at 0.1000000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 194403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 104191 mr = 140043 m= 44823 mr = 86235 m= 13878 mr = 37196 m= 3017 mr = 10980 m= 436 mr = 2267 m= 16 mr = 285 m= 0 mr = 8 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.380000 number of dielectric boundary points 83750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.520000 number of grid points assigned charge 15824 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) : 2.225093 object centre at (A) : 32.33100 13.68800 20.60000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1054785 -1.140158 midg,1,midg; midg,igrid,midg -0.2605637 -0.2872361 1,midg,midg; igrid,midg,midg -0.1152538 -3.2413237E-02 gauss-seidel spectral radius is 0.9993221 estimated iterations to convergence 303 setup time was (sec) 2.720000 now iterating at: 12:12:57 rms-change max change #iterations 11.14348 362.3301 at 10iterations 6.576955 121.3447 at 20iterations 3.898878 68.77598 at 30iterations 2.296288 43.96927 at 40iterations 1.353585 23.05024 at 50iterations 0.7998634 13.44212 at 60iterations 0.4704336 7.596207 at 70iterations 0.2770613 4.900558 at 80iterations 0.1630007 2.738115 at 90iterations 9.5860466E-02 1.736656 at 100iterations 5.6426007E-02 1.002025 at 110iterations 3.3209346E-02 0.5274854 at 120iterations 1.9563427E-02 0.2971344 at 130iterations 1.1463385E-02 0.1984344 at 140iterations 6.7703072E-03 0.1139507 at 150iterations 3.9760834E-03 6.2599182E-02 at 160iterations 2.3405799E-03 3.8395405E-02 at 170iterations 1.3766626E-03 2.2792459E-02 at 180iterations finished qdiffx linear iterations at : 12:13:14 total time elapsed so far: 19.00000 # loops : 180 mean,max change (kT/e) : 1.3766626E-03 2.2792459E-02 energy calculations done at 19.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.17000 DelPhi exited at 12:13:14 19.173u 0.498s 0:20.01 98.2% 0+0k 0+0io 0pf+0w