Sun Oct 9 12:00:48 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 9 2011 at 12:00:48 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6897888 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): -5.199000 43.61900 ymin,ymax (A): -14.28800 37.32200 zmin,zma (A): 1.310000 45.38600 x,y,z range (A): 48.81800 51.61000 44.07600 scale (grids/A): 0.6897888 object centre (A): 19.21000 11.51700 23.34800 number of atom coordinates read : 2374 total number of charged atoms : 2229 net assigned charge : 3.406019 assigned positive charge : 362.2741 centred at (gu) : 89.18428 90.81492 90.68861 assigned negative charge : -358.8686 centred at (gu) : 89.20805 90.98154 90.73764 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7600 nv = 96 ne = 84 npr = 48041 no. pairs analyzed = 48041 no. exposed pairs = 2911 no. arc points = 20457 no. surface atoms = 982 nbur = 1392 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 4249 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.2000000 number of dielectric boundary points 3755 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1965 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8640 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3084277E-08 6.6560307E-10 midg,1,midg; midg,igrid,midg 6.9235789E-08 -5.3239784E-08 1,midg,midg; igrid,midg,midg 3.3364774E-08 8.9450172E-09 gauss-seidel spectral radius is 0.9890797 estimated iterations to convergence 78 setup time was (sec) 0.4000000 now iterating at: 12:00:49 rms-change max change #iterations 0.1899391 26.90850 at 10iterations 2.3165377E-02 3.296335 at 20iterations 3.3133263E-03 0.5258789 at 30iterations 7.2890398E-04 0.1221695 at 40iterations 2.2405459E-04 3.6621094E-02 at 50iterations finished qdiffx linear iterations at : 12:00:52 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.2405459E-04 3.6621094E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 12:00:52 3.405u 0.162s 0:03.84 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 9 2011 at 12:00:52 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.069366 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): -5.199000 43.61900 ymin,ymax (A): -14.28800 37.32200 zmin,zma (A): 1.310000 45.38600 x,y,z range (A): 48.81800 51.61000 44.07600 scale (grids/A): 2.069366 object centre (A): 19.21000 11.51700 23.34800 number of atom coordinates read : 2374 total number of charged atoms : 2229 net assigned charge : 3.406019 assigned positive charge : 362.2741 centred at (gu) : 87.55242 92.44427 92.06532 assigned negative charge : -358.8686 centred at (gu) : 87.62381 92.94456 92.21273 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80534 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20457 grid for indexing accessible points = 1.400000 m= 30459 mr = 56034 m= 5157 mr = 22792 m= 423 mr = 3311 m= 3 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 3806 time to turn everything in is 0.4100000 number of dielectric boundary points 34236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17710 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) : 0.6897888 object centre at (A) : 19.21000 11.51700 23.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3488109E-02 1.4247453E-02 midg,1,midg; midg,igrid,midg 1.5123153E-02 -4.6692275E-02 1,midg,midg; igrid,midg,midg 4.6387665E-02 -1.0088675E-02 gauss-seidel spectral radius is 0.9988117 estimated iterations to convergence 230 setup time was (sec) 0.6400000 now iterating at: 12:00:53 rms-change max change #iterations 4.794563 196.9901 at 10iterations 2.358996 74.57649 at 20iterations 1.161311 39.75039 at 30iterations 0.5708084 16.00880 at 40iterations 0.2814981 8.849594 at 50iterations 0.1389431 4.075927 at 60iterations 6.8669774E-02 1.947259 at 70iterations 3.3906534E-02 1.095837 at 80iterations 1.6929563E-02 0.5122232 at 90iterations 8.4928777E-03 0.2496262 at 100iterations 4.3345327E-03 0.1423187 at 110iterations 2.2748411E-03 7.1617126E-02 at 120iterations finished qdiffx linear iterations at : 12:01:00 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.2748411E-03 7.1617126E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 12:01:00 7.902u 0.185s 0:08.35 96.7% 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 9 2011 at 12:01:00 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2374 !!! WARNING: GLM 182 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.104050 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): -5.199000 43.61900 ymin,ymax (A): -14.28800 37.32200 zmin,zma (A): 1.310000 45.38600 x,y,z range (A): 48.81800 51.61000 44.07600 scale (grids/A): 3.104050 object centre (A): 19.21000 11.51700 23.34800 number of atom coordinates read : 2374 total number of charged atoms : 2229 net assigned charge : 3.406019 assigned positive charge : 362.2741 centred at (gu) : 86.32854 93.66619 93.09799 assigned negative charge : -358.8686 centred at (gu) : 86.43576 94.41669 93.31911 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 185654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20457 grid for indexing accessible points = 1.400000 m= 96961 mr = 135324 m= 36849 mr = 79928 m= 9462 mr = 29989 m= 1736 mr = 7200 m= 180 mr = 1273 m= 2 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 12469 time to turn everything in is 1.200000 number of dielectric boundary points 77018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 17832 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) : 2.069366 object centre at (A) : 19.21000 11.51700 23.34800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4718504 2.8696246E-02 midg,1,midg; midg,igrid,midg 0.3294931 -0.5312405 1,midg,midg; igrid,midg,midg 0.4693365 -0.2935160 gauss-seidel spectral radius is 0.9992936 estimated iterations to convergence 297 setup time was (sec) 1.440000 now iterating at: 12:01:02 rms-change max change #iterations 10.78141 510.2963 at 10iterations 6.363269 132.3171 at 20iterations 3.748996 72.18167 at 30iterations 2.205384 43.28774 at 40iterations 1.294825 23.07361 at 50iterations 0.7596051 13.60902 at 60iterations 0.4452230 8.281736 at 70iterations 0.2607395 4.923643 at 80iterations 0.1525012 2.661267 at 90iterations 8.9338377E-02 1.540096 at 100iterations 5.2541744E-02 0.9224777 at 110iterations 3.0820737E-02 0.5735130 at 120iterations 1.8433150E-02 0.3167076 at 130iterations 1.1156382E-02 0.2194061 at 140iterations 6.9842697E-03 0.1333466 at 150iterations 4.5768893E-03 9.1123581E-02 at 160iterations 3.1869777E-03 6.5761566E-02 at 170iterations 2.3524074E-03 5.3958893E-02 at 180iterations finished qdiffx linear iterations at : 12:01:14 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 2.3524074E-03 5.3958893E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 12:01:14 13.130u 0.219s 0:13.64 97.8% 0+0k 0+0io 0pf+0w