Thu Mar 1 19:30:07 PST 2012 #!/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 Thu Mar 1 2012 at 19:30:07 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3246 !!! WARNING: SEP 61 has a net charge of -0.2750 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: 0.5983897 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): -2.483000 57.01000 ymin,ymax (A): -23.57600 26.93400 zmin,zma (A): -9.933001 45.28400 x,y,z range (A): 59.49300 50.51000 55.21700 scale (grids/A): 0.5983897 object centre (A): 27.26350 1.679000 17.67550 number of atom coordinates read : 3246 total number of charged atoms : 3100 net assigned charge : 4.225010 assigned positive charge : 487.0017 centred at (gu) : 91.92192 88.89729 90.13518 assigned negative charge : -482.7781 centred at (gu) : 91.94442 88.92680 90.13031 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7513 nv = 96 ne = 84 npr = 67473 no. pairs analyzed = 67473 no. exposed pairs = 3670 no. arc points = 25852 no. surface atoms = 1245 nbur = 2001 mkacc time = 0.1100000 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 = 1.456000 m= 339 mr = 4282 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2300000 number of dielectric boundary points 3552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2678 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4597865E-09 1.9799147E-09 midg,1,midg; midg,igrid,midg 3.8202144E-09 3.5916950E-10 1,midg,midg; igrid,midg,midg 1.7476397E-09 1.1064047E-09 gauss-seidel spectral radius is 0.9855935 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 19:30:08 rms-change max change #iterations 0.1190154 18.90624 at 10iterations 1.0174779E-02 1.344196 at 20iterations 8.8377780E-04 0.1231613 at 30iterations 8.6431523E-05 1.2858391E-02 at 40iterations 1.2167430E-05 1.8324852E-03 at 50iterations finished qdiffx linear iterations at : 19:30:11 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.2167430E-05 1.8324852E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 19:30:11 3.495u 0.177s 0:03.88 94.3% 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 Thu Mar 1 2012 at 19:30:11 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3246 !!! WARNING: SEP 61 has a net charge of -0.2750 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: 1.795169 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): -2.483000 57.01000 ymin,ymax (A): -23.57600 26.93400 zmin,zma (A): -9.933001 45.28400 x,y,z range (A): 59.49300 50.51000 55.21700 scale (grids/A): 1.795169 object centre (A): 27.26350 1.679000 17.67550 number of atom coordinates read : 3246 total number of charged atoms : 3100 net assigned charge : 4.225010 assigned positive charge : 487.0017 centred at (gu) : 95.76474 86.69077 90.40435 assigned negative charge : -482.7781 centred at (gu) : 95.83301 86.78014 90.39059 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25852 grid for indexing accessible points = 1.400000 m= 28361 mr = 60041 m= 3523 mr = 20626 m= 137 mr = 2037 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1554 time to turn everything in is 0.4000000 number of dielectric boundary points 32868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 24179 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) : 0.5983897 object centre at (A) : 27.26350 1.679000 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4556894E-04 -1.1703686E-02 midg,1,midg; midg,igrid,midg 6.5266830E-03 3.4980045E-03 1,midg,midg; igrid,midg,midg 3.0212535E-02 1.5475308E-02 gauss-seidel spectral radius is 0.9985207 estimated iterations to convergence 206 setup time was (sec) 0.6300000 now iterating at: 19:30:12 rms-change max change #iterations 4.228562 183.0925 at 10iterations 1.919876 97.79214 at 20iterations 0.8691245 28.03160 at 30iterations 0.3967306 12.59088 at 40iterations 0.1802055 5.626261 at 50iterations 8.2105525E-02 3.069844 at 60iterations 3.7254594E-02 1.238103 at 70iterations 1.6936665E-02 0.5535927 at 80iterations 7.7122860E-03 0.2353020 at 90iterations 3.5108288E-03 0.1044292 at 100iterations 1.6022287E-03 5.1864624E-02 at 110iterations 7.2845205E-04 2.1628499E-02 at 120iterations finished qdiffx linear iterations at : 19:30:19 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 7.2845205E-04 2.1628499E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 19:30:20 8.059u 0.281s 0:08.84 94.2% 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 Thu Mar 1 2012 at 19:30:20 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3246 !!! WARNING: SEP 61 has a net charge of -0.2750 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: 2.692754 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): -2.483000 57.01000 ymin,ymax (A): -23.57600 26.93400 zmin,zma (A): -9.933001 45.28400 x,y,z range (A): 59.49300 50.51000 55.21700 scale (grids/A): 2.692754 object centre (A): 27.26350 1.679000 17.67550 number of atom coordinates read : 3246 total number of charged atoms : 3100 net assigned charge : 4.225010 assigned positive charge : 487.0017 centred at (gu) : 98.64711 85.03614 90.60628 assigned negative charge : -482.7781 centred at (gu) : 98.74935 85.17007 90.58575 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 193843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25852 grid for indexing accessible points = 1.400000 m= 95462 mr = 145169 m= 30718 mr = 78240 m= 6105 mr = 24419 m= 558 mr = 4357 m= 16 mr = 270 m= 0 mr = 1 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 5070 time to turn everything in is 1.040000 number of dielectric boundary points 74246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 24791 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) : 1.795169 object centre at (A) : 27.26350 1.679000 17.67550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0948227E-02 -0.1951652 midg,1,midg; midg,igrid,midg 4.5268969E-03 5.6283053E-02 1,midg,midg; igrid,midg,midg 0.3566413 0.2932091 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.290000 now iterating at: 19:30:21 rms-change max change #iterations 10.13644 362.5876 at 10iterations 5.833673 111.0303 at 20iterations 3.336107 63.34441 at 30iterations 1.910679 33.66895 at 40iterations 1.089922 20.02398 at 50iterations 0.6220215 11.04285 at 60iterations 0.3551300 6.278875 at 70iterations 0.2022683 3.517250 at 80iterations 0.1150844 1.945297 at 90iterations 6.5607764E-02 1.088615 at 100iterations 3.7400007E-02 0.6262970 at 110iterations 2.1270240E-02 0.4254150 at 120iterations 1.2123458E-02 0.2060490 at 130iterations 6.9026910E-03 0.1288528 at 140iterations 3.9475015E-03 6.8721771E-02 at 150iterations 2.2580766E-03 3.8356304E-02 at 160iterations 1.2894006E-03 2.2036552E-02 at 170iterations 7.4145506E-04 1.3549805E-02 at 180iterations finished qdiffx linear iterations at : 19:30:33 total time elapsed so far: 13.08000 # loops : 180 mean,max change (kT/e) : 7.4145506E-04 1.3549805E-02 energy calculations done at 13.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.21000 DelPhi exited at 19:30:33 13.215u 0.238s 0:13.69 98.1% 0+0k 0+0io 0pf+0w