Mon Oct 10 14:15:27 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 Mon Oct 10 2011 at 14:15:27 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2470 !!! WARNING: ASL 359 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5583701 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): -10.40300 53.35400 ymin,ymax (A): 91.26100 144.6360 zmin,zma (A): 22.60100 68.36200 x,y,z range (A): 63.75700 53.37500 45.76100 scale (grids/A): 0.5583701 object centre (A): 21.47550 117.9485 45.48150 number of atom coordinates read : 2470 total number of charged atoms : 2321 net assigned charge : -0.5999959 assigned positive charge : 358.8441 centred at (gu) : 89.93066 89.14245 89.79481 assigned negative charge : -359.4447 centred at (gu) : 89.92633 89.18815 89.69563 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5199 nv = 96 ne = 84 npr = 47847 no. pairs analyzed = 47847 no. exposed pairs = 3473 no. arc points = 24957 no. surface atoms = 1153 nbur = 1317 mkacc time = 0.1700000 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= 244 mr = 2518 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2413 ## 286 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 6539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5717567E-10 7.2893014E-10 midg,1,midg; midg,igrid,midg 4.0011050E-10 -3.6485959E-10 1,midg,midg; igrid,midg,midg -9.9523757E-11 -2.4371097E-11 gauss-seidel spectral radius is 0.9834263 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 14:15:28 rms-change max change #iterations 7.0068181E-02 13.63384 at 10iterations 4.9993233E-03 0.9184418 at 20iterations 3.5546577E-04 6.1515808E-02 at 30iterations 2.5831423E-05 4.4708252E-03 at 40iterations 2.0035993E-06 3.1900406E-04 at 50iterations finished qdiffx linear iterations at : 14:15:31 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 2.0035993E-06 3.1900406E-04 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 14:15:32 4.474u 0.447s 0:05.54 88.6% 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 Mon Oct 10 2011 at 14:15:32 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2470 !!! WARNING: ASL 359 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.675110 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): -10.40300 53.35400 ymin,ymax (A): 91.26100 144.6360 zmin,zma (A): 22.60100 68.36200 x,y,z range (A): 63.75700 53.37500 45.76100 scale (grids/A): 1.675110 object centre (A): 21.47550 117.9485 45.48150 number of atom coordinates read : 2470 total number of charged atoms : 2321 net assigned charge : -0.5999959 assigned positive charge : 358.8441 centred at (gu) : 89.79139 87.42692 89.38374 assigned negative charge : -359.4447 centred at (gu) : 89.77882 87.56408 89.08666 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 56266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24957 grid for indexing accessible points = 1.400000 m= 18343 mr = 36047 m= 2329 mr = 12753 m= 74 mr = 1191 m= 0 mr = 9 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 27012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17870 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) : 0.5583701 object centre at (A) : 21.47550 117.9485 45.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8031610E-03 4.8011276E-03 midg,1,midg; midg,igrid,midg -3.9385683E-03 -7.0834588E-03 1,midg,midg; igrid,midg,midg -9.3975095E-03 1.8162906E-02 gauss-seidel spectral radius is 0.9982386 estimated iterations to convergence 189 setup time was (sec) 0.9000000 now iterating at: 14:15:34 rms-change max change #iterations 3.088912 139.3774 at 10iterations 1.299098 55.00210 at 20iterations 0.5489907 20.71636 at 30iterations 0.2311173 9.657660 at 40iterations 9.7082496E-02 3.768955 at 50iterations 4.0917493E-02 1.596354 at 60iterations 1.7374694E-02 0.6664906 at 70iterations 7.2781676E-03 0.2785721 at 80iterations 3.0935165E-03 0.1349907 at 90iterations 1.3051325E-03 4.7141075E-02 at 100iterations 5.4971268E-04 1.9758940E-02 at 110iterations 2.3377102E-04 1.0822296E-02 at 120iterations finished qdiffx linear iterations at : 14:15:43 total time elapsed so far: 9.760000 # loops : 120 mean,max change (kT/e) : 2.3377102E-04 1.0822296E-02 energy calculations done at 9.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.980000 DelPhi exited at 14:15:43 9.980u 0.476s 0:10.98 95.1% 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 Mon Oct 10 2011 at 14:15:43 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2470 !!! WARNING: ASL 359 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.512665 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): -10.40300 53.35400 ymin,ymax (A): 91.26100 144.6360 zmin,zma (A): 22.60100 68.36200 x,y,z range (A): 63.75700 53.37500 45.76100 scale (grids/A): 2.512665 object centre (A): 21.47550 117.9485 45.48150 number of atom coordinates read : 2470 total number of charged atoms : 2321 net assigned charge : -0.5999959 assigned positive charge : 358.8441 centred at (gu) : 89.68703 86.14018 89.07558 assigned negative charge : -359.4447 centred at (gu) : 89.66813 86.34615 88.62997 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 130281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24957 grid for indexing accessible points = 1.400000 m= 61058 mr = 88773 m= 19962 mr = 47683 m= 3780 mr = 15244 m= 341 mr = 2571 m= 3 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.470000 number of dielectric boundary points 60992 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 18555 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) : 1.675110 object centre at (A) : 21.47550 117.9485 45.48150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7472084E-02 7.6338924E-02 midg,1,midg; midg,igrid,midg -7.4937947E-02 -7.4194610E-02 1,midg,midg; igrid,midg,midg -0.1203813 0.5710748 gauss-seidel spectral radius is 0.9991522 estimated iterations to convergence 271 setup time was (sec) 1.850000 now iterating at: 14:15:46 rms-change max change #iterations 8.131134 355.3082 at 10iterations 4.642676 159.2069 at 20iterations 2.621745 68.24622 at 30iterations 1.477752 39.19833 at 40iterations 0.8267910 21.39320 at 50iterations 0.4621966 10.50417 at 60iterations 0.2573574 6.008750 at 70iterations 0.1435033 3.136968 at 80iterations 7.9509750E-02 1.886180 at 90iterations 4.4024728E-02 1.106711 at 100iterations 2.4381597E-02 0.5334244 at 110iterations 1.3499582E-02 0.3009791 at 120iterations 7.4812230E-03 0.1604481 at 130iterations 4.1307723E-03 9.0568542E-02 at 140iterations 2.2826083E-03 5.3741932E-02 at 150iterations 1.2617109E-03 2.9277802E-02 at 160iterations 6.9585873E-04 1.5260696E-02 at 170iterations 3.8350272E-04 9.4223022E-03 at 180iterations finished qdiffx linear iterations at : 14:16:04 total time elapsed so far: 20.23000 # loops : 180 mean,max change (kT/e) : 3.8350272E-04 9.4223022E-03 energy calculations done at 20.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.46000 DelPhi exited at 14:16:05 20.469u 0.495s 0:21.49 97.4% 0+0k 0+0io 0pf+0w