Sat Oct 15 11:19:11 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 11:19:11 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3585 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: HIR 235 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5685993 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): 12.02000 74.63000 ymin,ymax (A): -1.283000 50.94100 zmin,zma (A): 22.51600 77.60700 x,y,z range (A): 62.61000 52.22400 55.09100 scale (grids/A): 0.5685993 object centre (A): 43.32500 24.82900 50.06150 number of atom coordinates read : 3585 total number of charged atoms : 3465 net assigned charge : -3.457974 assigned positive charge : 553.6507 centred at (gu) : 88.40678 91.21112 89.53493 assigned negative charge : -557.1102 centred at (gu) : 88.49937 91.06923 89.52279 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7462 nv = 96 ne = 84 npr = 73256 no. pairs analyzed = 73256 no. exposed pairs = 4107 no. arc points = 28583 no. surface atoms = 1390 nbur = 2195 mkacc time = 0.2500000 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 = 1.512000 m= 271 mr = 4237 m= 0 mr = 15 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.5000000 number of dielectric boundary points 3481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2841 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 9660 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.8420760E-10 -3.0472047E-10 midg,1,midg; midg,igrid,midg -2.4422293E-09 2.7549099E-09 1,midg,midg; igrid,midg,midg 1.7077689E-09 -1.5846369E-09 gauss-seidel spectral radius is 0.9840798 estimated iterations to convergence 65 setup time was (sec) 0.8700000 now iterating at: 11:19:12 rms-change max change #iterations 0.1044815 16.20673 at 10iterations 7.8721130E-03 1.080711 at 20iterations 5.9943821E-04 8.1607819E-02 at 30iterations 4.9799495E-05 7.7424049E-03 at 40iterations 6.3575621E-06 1.1291504E-03 at 50iterations finished qdiffx linear iterations at : 11:19:16 total time elapsed so far: 5.080000 # loops : 50 mean,max change (kT/e) : 6.3575621E-06 1.1291504E-03 energy calculations done at 5.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 11:19:17 5.306u 0.411s 0:06.01 95.0% 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 11:19:17 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3585 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: HIR 235 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.705798 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): 12.02000 74.63000 ymin,ymax (A): -1.283000 50.94100 zmin,zma (A): 22.51600 77.60700 x,y,z range (A): 62.61000 52.22400 55.09100 scale (grids/A): 1.705798 object centre (A): 43.32500 24.82900 50.06150 number of atom coordinates read : 3585 total number of charged atoms : 3465 net assigned charge : -3.457974 assigned positive charge : 553.6507 centred at (gu) : 85.21945 93.63225 88.60397 assigned negative charge : -557.1102 centred at (gu) : 85.49779 93.20711 88.56793 start vw surface at 0.2000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 82947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28583 grid for indexing accessible points = 1.400000 m= 27500 mr = 59187 m= 3019 mr = 20424 m= 98 mr = 1699 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 2278 time to turn everything in is 0.8400000 number of dielectric boundary points 32228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 26818 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) : 0.5685993 object centre at (A) : 43.32500 24.82900 50.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1408867E-02 -6.9998815E-03 midg,1,midg; midg,igrid,midg -1.6262671E-02 1.5258156E-02 1,midg,midg; igrid,midg,midg 7.2202650E-03 -8.1851706E-03 gauss-seidel spectral radius is 0.9983913 estimated iterations to convergence 198 setup time was (sec) 1.210000 now iterating at: 11:19:19 rms-change max change #iterations 4.161543 158.0371 at 10iterations 1.831350 53.44027 at 20iterations 0.8043251 26.05618 at 30iterations 0.3538818 12.82807 at 40iterations 0.1557158 5.020672 at 50iterations 6.8502747E-02 2.099158 at 60iterations 3.0153638E-02 0.9257030 at 70iterations 1.3231346E-02 0.4146156 at 80iterations 5.8412892E-03 0.2011584 at 90iterations 2.5655755E-03 8.9027882E-02 at 100iterations 1.1299629E-03 3.6791086E-02 at 110iterations 4.9753516E-04 1.6143799E-02 at 120iterations finished qdiffx linear iterations at : 11:19:30 total time elapsed so far: 12.11000 # loops : 120 mean,max change (kT/e) : 4.9753516E-04 1.6143799E-02 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 11:19:30 12.332u 0.477s 0:13.33 96.0% 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 11:19:30 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3585 !!! WARNING: HIR 14 has a net charge of 0.5140 !!! WARNING: HIR 211 has a net charge of 0.5140 !!! WARNING: HIR 235 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.558697 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): 12.02000 74.63000 ymin,ymax (A): -1.283000 50.94100 zmin,zma (A): 22.51600 77.60700 x,y,z range (A): 62.61000 52.22400 55.09100 scale (grids/A): 2.558697 object centre (A): 43.32500 24.82900 50.06150 number of atom coordinates read : 3585 total number of charged atoms : 3465 net assigned charge : -3.457974 assigned positive charge : 553.6507 centred at (gu) : 82.82876 95.44830 87.90546 assigned negative charge : -557.1102 centred at (gu) : 83.24657 94.81066 87.85166 start vw surface at 0.1800000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 192882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28583 grid for indexing accessible points = 1.400000 m= 93411 mr = 143872 m= 28775 mr = 77081 m= 5054 mr = 23134 m= 412 mr = 3614 m= 14 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 7378 time to turn everything in is 2.100000 number of dielectric boundary points 72603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 2.270000 number of grid points assigned charge 27700 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) : 1.705798 object centre at (A) : 43.32500 24.82900 50.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1953246 -0.1122880 midg,1,midg; midg,igrid,midg -0.1817565 0.1461637 1,midg,midg; igrid,midg,midg 6.0200922E-02 -4.6479039E-02 gauss-seidel spectral radius is 0.9992005 estimated iterations to convergence 279 setup time was (sec) 2.490000 now iterating at: 11:19:33 rms-change max change #iterations 10.22661 277.3752 at 10iterations 5.817642 124.1031 at 20iterations 3.291863 73.40720 at 30iterations 1.865365 38.57236 at 40iterations 1.049815 20.95718 at 50iterations 0.5920775 11.55685 at 60iterations 0.3330049 6.150781 at 70iterations 0.1871949 3.323190 at 80iterations 0.1054194 1.896365 at 90iterations 5.9196796E-02 1.184213 at 100iterations 3.3282984E-02 0.6148052 at 110iterations 1.8731335E-02 0.3672562 at 120iterations 1.0551367E-02 0.1921997 at 130iterations 5.9291106E-03 0.1091232 at 140iterations 3.3286850E-03 5.7349205E-02 at 150iterations 1.8700095E-03 3.4812927E-02 at 160iterations 1.0513958E-03 1.8465877E-02 at 170iterations 5.9069990E-04 1.1104584E-02 at 180iterations finished qdiffx linear iterations at : 11:19:52 total time elapsed so far: 20.95000 # loops : 180 mean,max change (kT/e) : 5.9069990E-04 1.1104584E-02 energy calculations done at 20.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.16000 DelPhi exited at 11:19:52 21.169u 0.519s 0:21.95 98.7% 0+0k 0+0io 0pf+0w