Sun Oct 9 17:28:29 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 Sun Oct 9 2011 at 17:28:29 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5639872 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): 3.211000 64.99900 ymin,ymax (A): -8.642000 53.45100 zmin,zma (A): -1.167000 61.95500 x,y,z range (A): 61.78800 62.09300 63.12200 scale (grids/A): 0.5639872 object centre (A): 34.10500 22.40450 30.39400 number of atom coordinates read : 5005 total number of charged atoms : 4860 net assigned charge : 0.1210452 assigned positive charge : 768.0857 centred at (gu) : 88.34148 89.25082 89.15617 assigned negative charge : -767.9705 centred at (gu) : 88.23798 89.28742 89.12810 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10453 nv = 96 ne = 84 npr = 101183 no. pairs analyzed = 101183 no. exposed pairs = 5941 no. arc points = 40017 no. surface atoms = 2023 nbur = 2982 mkacc time = 0.2100000 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= 487 mr = 6000 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 4917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4059 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 13602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8984551E-10 5.4612082E-10 midg,1,midg; midg,igrid,midg 1.0289165E-09 -6.2409666E-10 1,midg,midg; igrid,midg,midg -3.3775469E-09 1.5385880E-09 gauss-seidel spectral radius is 0.9839317 estimated iterations to convergence 65 setup time was (sec) 0.7100000 now iterating at: 17:28:30 rms-change max change #iterations 0.1187825 14.90280 at 10iterations 1.0784550E-02 1.379486 at 20iterations 2.8908744E-03 0.3181839 at 30iterations 1.3425827E-03 0.1410904 at 40iterations 6.5789529E-04 7.5316429E-02 at 50iterations finished qdiffx linear iterations at : 17:28:33 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 6.5789529E-04 7.5316429E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 17:28:33 3.530u 0.218s 0:04.02 93.0% 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 Sun Oct 9 2011 at 17:28:33 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.691962 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): 3.211000 64.99900 ymin,ymax (A): -8.642000 53.45100 zmin,zma (A): -1.167000 61.95500 x,y,z range (A): 61.78800 62.09300 63.12200 scale (grids/A): 1.691962 object centre (A): 34.10500 22.40450 30.39400 number of atom coordinates read : 5005 total number of charged atoms : 4860 net assigned charge : 0.1210452 assigned positive charge : 768.0857 centred at (gu) : 85.02290 87.75103 87.46717 assigned negative charge : -767.9705 centred at (gu) : 84.71369 87.86236 87.38423 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 116481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40017 grid for indexing accessible points = 1.400000 m= 41450 mr = 84523 m= 5301 mr = 30131 m= 177 mr = 2913 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7800000 number of dielectric boundary points 45815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 350 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 37473 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) : 0.5639872 object centre at (A) : 34.10500 22.40450 30.39400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7283406E-02 -2.9960517E-02 midg,1,midg; midg,igrid,midg 1.9683210E-02 9.1126719E-03 1,midg,midg; igrid,midg,midg -1.9978609E-02 2.8408187E-02 gauss-seidel spectral radius is 0.9984984 estimated iterations to convergence 205 setup time was (sec) 1.090000 now iterating at: 17:28:35 rms-change max change #iterations 4.970167 211.1880 at 10iterations 2.237784 77.08955 at 20iterations 1.013977 30.00500 at 30iterations 0.4588748 12.80786 at 40iterations 0.2073720 5.608370 at 50iterations 9.4518058E-02 2.562361 at 60iterations 4.3124396E-02 1.217392 at 70iterations 2.0095944E-02 0.5960722 at 80iterations 9.8334635E-03 0.2787933 at 90iterations 5.3058313E-03 0.1400986 at 100iterations 3.2601012E-03 8.6662292E-02 at 110iterations 2.2681179E-03 5.5836201E-02 at 120iterations finished qdiffx linear iterations at : 17:28:42 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 2.2681179E-03 5.5836201E-02 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 17:28:42 8.139u 0.253s 0:08.67 96.6% 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 Sun Oct 9 2011 at 17:28:42 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5005 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.537942 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): 3.211000 64.99900 ymin,ymax (A): -8.642000 53.45100 zmin,zma (A): -1.167000 61.95500 x,y,z range (A): 61.78800 62.09300 63.12200 scale (grids/A): 2.537942 object centre (A): 34.10500 22.40450 30.39400 number of atom coordinates read : 5005 total number of charged atoms : 4860 net assigned charge : 0.1210452 assigned positive charge : 768.0857 centred at (gu) : 82.53387 86.62608 86.20045 assigned negative charge : -767.9705 centred at (gu) : 82.07044 86.79348 86.07629 start vw surface at 0.2000000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 270470 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40017 grid for indexing accessible points = 1.400000 m= 138369 mr = 205231 m= 45336 mr = 113037 m= 8770 mr = 35482 m= 838 mr = 6106 m= 25 mr = 441 m= 0 mr = 2 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 103509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 38852 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) : 1.691962 object centre at (A) : 34.10500 22.40450 30.39400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4158019 -0.7167809 midg,1,midg; midg,igrid,midg 2.7185362E-03 -9.9335574E-03 1,midg,midg; igrid,midg,midg -0.3884025 0.3210724 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 2.330000 now iterating at: 17:28:45 rms-change max change #iterations 12.51496 307.4210 at 10iterations 7.432212 161.0455 at 20iterations 4.383875 85.61202 at 30iterations 2.582225 43.02264 at 40iterations 1.511022 25.59979 at 50iterations 0.8834481 16.90869 at 60iterations 0.5148076 8.255508 at 70iterations 0.2999972 4.766331 at 80iterations 0.1744788 2.848886 at 90iterations 0.1014200 1.616875 at 100iterations 5.8975615E-02 0.9766426 at 110iterations 3.4444969E-02 0.5707016 at 120iterations 2.0249089E-02 0.3192196 at 130iterations 1.2110772E-02 0.1962643 at 140iterations 7.4793659E-03 0.1251583 at 150iterations 4.8572393E-03 8.3407402E-02 at 160iterations 3.3867040E-03 5.5384636E-02 at 170iterations 2.5445833E-03 4.0473938E-02 at 180iterations finished qdiffx linear iterations at : 17:28:56 total time elapsed so far: 13.80000 # loops : 180 mean,max change (kT/e) : 2.5445833E-03 4.0473938E-02 energy calculations done at 13.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.99000 DelPhi exited at 17:28:57 13.997u 0.259s 0:14.54 97.9% 0+0k 0+0io 0pf+0w