Sat Oct 15 12:12:57 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 15 2011 at 12:12:57 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6543757 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): -27.34200 27.06100 ymin,ymax (A): 8.113999 52.10300 zmin,zma (A): -12.60500 41.37900 x,y,z range (A): 54.40300 43.98900 53.98400 scale (grids/A): 0.6543757 object centre (A): -0.1405010 30.10850 14.38700 number of atom coordinates read : 2283 total number of charged atoms : 2149 net assigned charge : 10.51402 assigned positive charge : 333.5077 centred at (gu) : 90.56470 90.53393 91.31720 assigned negative charge : -322.9942 centred at (gu) : 90.56426 90.47851 91.30019 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6762 nv = 96 ne = 84 npr = 45564 no. pairs analyzed = 45564 no. exposed pairs = 3095 no. arc points = 22410 no. surface atoms = 1039 nbur = 1244 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3459 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.1900000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2153 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5671917E-08 3.3017798E-08 midg,1,midg; midg,igrid,midg 1.3400595E-08 3.4182136E-08 1,midg,midg; igrid,midg,midg 2.0289413E-08 2.5631303E-08 gauss-seidel spectral radius is 0.9878796 estimated iterations to convergence 74 setup time was (sec) 0.4300000 now iterating at: 12:12:58 rms-change max change #iterations 0.1454123 21.31609 at 10iterations 1.4666539E-02 2.109070 at 20iterations 1.5603529E-03 0.3233329 at 30iterations 1.6263373E-04 2.2289276E-02 at 40iterations 1.7411347E-05 2.6884079E-03 at 50iterations finished qdiffx linear iterations at : 12:13:01 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.7411347E-05 2.6884079E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 12:13:02 4.002u 0.247s 0:04.58 92.5% 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 Sat Oct 15 2011 at 12:13:02 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.963127 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): -27.34200 27.06100 ymin,ymax (A): 8.113999 52.10300 zmin,zma (A): -12.60500 41.37900 x,y,z range (A): 54.40300 43.98900 53.98400 scale (grids/A): 1.963127 object centre (A): -0.1405010 30.10850 14.38700 number of atom coordinates read : 2283 total number of charged atoms : 2149 net assigned charge : 10.51402 assigned positive charge : 333.5077 centred at (gu) : 91.69394 91.60178 93.95149 assigned negative charge : -322.9942 centred at (gu) : 91.69302 91.43567 93.90099 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72221 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22410 grid for indexing accessible points = 1.400000 m= 25620 mr = 47703 m= 4174 mr = 18226 m= 263 mr = 2395 m= 6 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 348 time to turn everything in is 0.3700000 number of dielectric boundary points 33869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 16953 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) : 0.6543757 object centre at (A) : -0.1405010 30.10850 14.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9469723E-02 3.4082960E-02 midg,1,midg; midg,igrid,midg -5.1586219E-04 2.3037532E-02 1,midg,midg; igrid,midg,midg 5.1486097E-02 6.1389256E-02 gauss-seidel spectral radius is 0.9986929 estimated iterations to convergence 219 setup time was (sec) 0.6100000 now iterating at: 12:13:02 rms-change max change #iterations 4.090015 193.5743 at 10iterations 1.940237 69.92314 at 20iterations 0.9188633 28.43574 at 30iterations 0.4379631 14.27118 at 40iterations 0.2077243 6.521911 at 50iterations 9.8783925E-02 3.307066 at 60iterations 4.6806339E-02 1.500717 at 70iterations 2.2376979E-02 0.6798732 at 80iterations 1.0595894E-02 0.3302002 at 90iterations 5.0499486E-03 0.1570864 at 100iterations 2.3895041E-03 7.2215557E-02 at 110iterations 1.1400597E-03 3.8302422E-02 at 120iterations finished qdiffx linear iterations at : 12:13:10 total time elapsed so far: 8.370000 # loops : 120 mean,max change (kT/e) : 1.1400597E-03 3.8302422E-02 energy calculations done at 8.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.500000 DelPhi exited at 12:13:11 8.501u 0.277s 0:09.10 96.3% 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 12:13:11 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2283 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.944690 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): -27.34200 27.06100 ymin,ymax (A): 8.113999 52.10300 zmin,zma (A): -12.60500 41.37900 x,y,z range (A): 54.40300 43.98900 53.98400 scale (grids/A): 2.944690 object centre (A): -0.1405010 30.10850 14.38700 number of atom coordinates read : 2283 total number of charged atoms : 2149 net assigned charge : 10.51402 assigned positive charge : 333.5077 centred at (gu) : 92.54076 92.40258 95.92715 assigned negative charge : -322.9942 centred at (gu) : 92.53962 92.15349 95.85153 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 166409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22410 grid for indexing accessible points = 1.400000 m= 82401 mr = 116022 m= 29909 mr = 65697 m= 7318 mr = 23247 m= 1191 mr = 5241 m= 62 mr = 749 m= 0 mr = 13 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 0.9900000 number of dielectric boundary points 76321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 17189 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) : 1.963127 object centre at (A) : -0.1405010 30.10850 14.38700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6212687 0.3662060 midg,1,midg; midg,igrid,midg 8.8214997E-04 0.2151971 1,midg,midg; igrid,midg,midg 0.5498683 0.6002865 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 1.270000 now iterating at: 12:13:12 rms-change max change #iterations 9.690913 422.2545 at 10iterations 5.739440 149.1362 at 20iterations 3.387241 78.35082 at 30iterations 1.989108 45.68668 at 40iterations 1.164813 32.16811 at 50iterations 0.6810513 14.86049 at 60iterations 0.3979994 9.077978 at 70iterations 0.2308832 4.316803 at 80iterations 0.1344523 2.636896 at 90iterations 7.8089550E-02 1.552697 at 100iterations 4.5509931E-02 0.9047090 at 110iterations 2.6415884E-02 0.5222576 at 120iterations 1.5284387E-02 0.3067245 at 130iterations 8.8853482E-03 0.1723289 at 140iterations 5.1529850E-03 0.1034427 at 150iterations 2.9937334E-03 5.5217743E-02 at 160iterations 1.7319950E-03 3.3199310E-02 at 170iterations 1.0080029E-03 1.8302917E-02 at 180iterations finished qdiffx linear iterations at : 12:13:26 total time elapsed so far: 14.63000 # loops : 180 mean,max change (kT/e) : 1.0080029E-03 1.8302917E-02 energy calculations done at 14.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.76000 DelPhi exited at 12:13:26 14.764u 0.292s 0:15.39 97.7% 0+0k 0+0io 0pf+0w