Sat Oct 8 17:15:07 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 8 2011 at 17:15:07 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 = 3399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5634695 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): 35.94400 94.95600 ymin,ymax (A): 16.03600 79.21600 zmin,zma (A): -24.72900 27.56100 x,y,z range (A): 59.01200 63.18000 52.29000 scale (grids/A): 0.5634695 object centre (A): 65.45000 47.62600 1.415999 number of atom coordinates read : 3399 total number of charged atoms : 3253 net assigned charge : -5.999988 assigned positive charge : 509.6025 centred at (gu) : 89.66170 90.10899 89.71813 assigned negative charge : -515.6038 centred at (gu) : 89.66931 90.07799 89.69638 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7038 nv = 96 ne = 84 npr = 69205 no. pairs analyzed = 69205 no. exposed pairs = 4128 no. arc points = 28200 no. surface atoms = 1401 nbur = 1998 mkacc time = 0.1900000 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 = 1.540000 m= 285 mr = 3866 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2968 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1151452E-09 -3.8555989E-10 midg,1,midg; midg,igrid,midg -1.1484073E-09 -2.8345878E-10 1,midg,midg; igrid,midg,midg -6.6554195E-10 -7.7309953E-10 gauss-seidel spectral radius is 0.9837799 estimated iterations to convergence 65 setup time was (sec) 0.7200000 now iterating at: 17:15:08 rms-change max change #iterations 9.1146536E-02 14.35142 at 10iterations 6.7459103E-03 0.9990559 at 20iterations 5.6943885E-04 8.5651398E-02 at 30iterations 8.1216160E-05 1.4984131E-02 at 40iterations 1.9031801E-05 3.8757324E-03 at 50iterations finished qdiffx linear iterations at : 17:15:11 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 1.9031801E-05 3.8757324E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 17:15:12 4.290u 0.258s 0:04.82 94.1% 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 8 2011 at 17:15:12 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 = 3399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.690408 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): 35.94400 94.95600 ymin,ymax (A): 16.03600 79.21600 zmin,zma (A): -24.72900 27.56100 x,y,z range (A): 59.01200 63.18000 52.29000 scale (grids/A): 1.690408 object centre (A): 65.45000 47.62600 1.415999 number of atom coordinates read : 3399 total number of charged atoms : 3253 net assigned charge : -5.999988 assigned positive charge : 509.6025 centred at (gu) : 88.98403 90.32599 89.15364 assigned negative charge : -515.6038 centred at (gu) : 89.00770 90.23343 89.08883 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77801 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 25829 mr = 54619 m= 2863 mr = 18402 m= 89 mr = 1506 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 0.7100000 number of dielectric boundary points 32046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 25115 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) : 0.5634695 object centre at (A) : 65.45000 47.62600 1.415999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0365080E-03 -7.9463776E-03 midg,1,midg; midg,igrid,midg 3.5080477E-03 1.4369000E-02 1,midg,midg; igrid,midg,midg -2.0789554E-02 -7.7777947E-03 gauss-seidel spectral radius is 0.9983450 estimated iterations to convergence 195 setup time was (sec) 1.020000 now iterating at: 17:15:13 rms-change max change #iterations 3.858551 157.0468 at 10iterations 1.672372 53.75618 at 20iterations 0.7241387 22.14306 at 30iterations 0.3148507 10.32524 at 40iterations 0.1369058 4.476162 at 50iterations 5.9454158E-02 1.879912 at 60iterations 2.5938500E-02 0.8714066 at 70iterations 1.1273909E-02 0.3403206 at 80iterations 4.9184198E-03 0.1544375 at 90iterations 2.1487356E-03 7.1006477E-02 at 100iterations 9.4740471E-04 2.8484941E-02 at 110iterations 4.2536057E-04 1.4020920E-02 at 120iterations finished qdiffx linear iterations at : 17:15:22 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 4.2536057E-04 1.4020920E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 17:15:22 9.836u 0.313s 0:10.42 97.3% 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 8 2011 at 17:15:22 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 = 3399 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.535613 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): 35.94400 94.95600 ymin,ymax (A): 16.03600 79.21600 zmin,zma (A): -24.72900 27.56100 x,y,z range (A): 59.01200 63.18000 52.29000 scale (grids/A): 2.535613 object centre (A): 65.45000 47.62600 1.415999 number of atom coordinates read : 3399 total number of charged atoms : 3253 net assigned charge : -5.999988 assigned positive charge : 509.6025 centred at (gu) : 88.47601 90.48882 88.73030 assigned negative charge : -515.6038 centred at (gu) : 88.51130 90.34995 88.63324 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 180347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28200 grid for indexing accessible points = 1.400000 m= 88044 mr = 132705 m= 26426 mr = 71187 m= 4679 mr = 20459 m= 391 mr = 3155 m= 8 mr = 197 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 435 time to turn everything in is 1.710000 number of dielectric boundary points 72192 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 26013 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) : 1.690408 object centre at (A) : 65.45000 47.62600 1.415999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5107605E-02 -8.4025703E-02 midg,1,midg; midg,igrid,midg 0.3172908 0.3335404 1,midg,midg; igrid,midg,midg -0.2662892 -7.2133549E-02 gauss-seidel spectral radius is 0.9991930 estimated iterations to convergence 278 setup time was (sec) 2.060000 now iterating at: 17:15:24 rms-change max change #iterations 9.759325 361.9368 at 10iterations 5.584721 145.9825 at 20iterations 3.174362 74.46385 at 30iterations 1.798750 34.14380 at 40iterations 1.014319 21.67002 at 50iterations 0.5746111 12.35127 at 60iterations 0.3229902 6.855764 at 70iterations 0.1812365 3.705368 at 80iterations 0.1018119 2.016984 at 90iterations 5.7270873E-02 1.066607 at 100iterations 3.2148782E-02 0.6293182 at 110iterations 1.8040827E-02 0.3338966 at 120iterations 1.0142462E-02 0.1859264 at 130iterations 5.6843911E-03 0.1091995 at 140iterations 3.1976653E-03 6.7144394E-02 at 150iterations 1.7968883E-03 3.3696175E-02 at 160iterations 1.0175329E-03 2.3284078E-02 at 170iterations 5.7833683E-04 1.0105133E-02 at 180iterations finished qdiffx linear iterations at : 17:15:39 total time elapsed so far: 16.11000 # loops : 180 mean,max change (kT/e) : 5.7833683E-04 1.0105133E-02 energy calculations done at 16.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.29000 DelPhi exited at 17:15:39 16.289u 0.351s 0:16.90 98.4% 0+0k 0+0io 0pf+0w