Sun Oct 9 23:46:51 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 23:46:52 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5948303 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): -29.30700 30.54200 ymin,ymax (A): 7.945000 61.80400 zmin,zma (A): 24.92800 77.25300 x,y,z range (A): 59.84900 53.85900 52.32500 scale (grids/A): 0.5948303 object centre (A): 0.6175003 34.87450 51.09050 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -0.9749913 assigned positive charge : 471.7190 centred at (gu) : 89.72005 89.06487 88.99940 assigned negative charge : -472.6952 centred at (gu) : 89.77280 89.07166 89.10988 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7399 nv = 96 ne = 84 npr = 62331 no. pairs analyzed = 62331 no. exposed pairs = 4079 no. arc points = 28991 no. surface atoms = 1355 nbur = 1778 mkacc time = 0.1400000 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= 342 mr = 3892 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3300000 number of dielectric boundary points 3833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2880 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9320 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7003734E-09 -3.6754924E-09 midg,1,midg; midg,igrid,midg -1.8001015E-10 -5.3600552E-10 1,midg,midg; igrid,midg,midg 1.6824392E-09 -2.2583366E-09 gauss-seidel spectral radius is 0.9854257 estimated iterations to convergence 68 setup time was (sec) 0.5700000 now iterating at: 23:46:52 rms-change max change #iterations 0.1162578 17.38969 at 10iterations 9.7318152E-03 1.423463 at 20iterations 7.9765794E-04 0.1227493 at 30iterations 6.9120164E-05 1.0181427E-02 at 40iterations 6.5918166E-06 8.6736679E-04 at 50iterations finished qdiffx linear iterations at : 23:46:55 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 6.5918166E-06 8.6736679E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 23:46:55 3.394u 0.196s 0:03.86 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 23:46:55 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: SEP 138 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.784491 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): -29.30700 30.54200 ymin,ymax (A): 7.945000 61.80400 zmin,zma (A): 24.92800 77.25300 x,y,z range (A): 59.84900 53.85900 52.32500 scale (grids/A): 1.784491 object centre (A): 0.6175003 34.87450 51.09050 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -0.9749913 assigned positive charge : 471.7190 centred at (gu) : 89.15925 87.19366 86.99754 assigned negative charge : -472.6952 centred at (gu) : 89.31779 87.21487 87.32967 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 81037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28991 grid for indexing accessible points = 1.400000 m= 26005 mr = 55232 m= 3141 mr = 18059 m= 92 mr = 1661 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1588 time to turn everything in is 0.6000000 number of dielectric boundary points 35319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 23289 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) : 0.5948303 object centre at (A) : 0.6175003 34.87450 51.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0115079E-02 -5.9155221E-03 midg,1,midg; midg,igrid,midg 6.1540660E-03 5.9987423E-03 1,midg,midg; igrid,midg,midg 1.3124851E-02 -1.2514001E-02 gauss-seidel spectral radius is 0.9985154 estimated iterations to convergence 206 setup time was (sec) 0.9000000 now iterating at: 23:46:57 rms-change max change #iterations 4.189471 159.2326 at 10iterations 1.885067 67.15138 at 20iterations 0.8532162 29.66894 at 30iterations 0.3864197 14.07557 at 40iterations 0.1749721 5.569390 at 50iterations 7.9390325E-02 2.401451 at 60iterations 3.5848461E-02 1.162781 at 70iterations 1.6245514E-02 0.5309200 at 80iterations 7.3733744E-03 0.2526035 at 90iterations 3.3476281E-03 0.1089745 at 100iterations 1.5183756E-03 5.1567078E-02 at 110iterations 6.8890239E-04 2.1743774E-02 at 120iterations finished qdiffx linear iterations at : 23:47:04 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 6.8890239E-04 2.1743774E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 23:47:04 8.132u 0.209s 0:08.69 95.8% 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 23:47:04 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 2.676737 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): -29.30700 30.54200 ymin,ymax (A): 7.945000 61.80400 zmin,zma (A): 24.92800 77.25300 x,y,z range (A): 59.84900 53.85900 52.32500 scale (grids/A): 2.676737 object centre (A): 0.6175003 34.87450 51.09050 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -0.9749913 assigned positive charge : 471.7190 centred at (gu) : 88.73867 85.79018 85.49596 assigned negative charge : -472.6952 centred at (gu) : 88.97658 85.82219 85.99442 start vw surface at 0.2100000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 188152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28991 grid for indexing accessible points = 1.400000 m= 88132 mr = 134691 m= 27024 mr = 70184 m= 5154 mr = 20588 m= 473 mr = 3516 m= 10 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 5286 time to turn everything in is 1.540000 number of dielectric boundary points 79718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 23883 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) : 1.784491 object centre at (A) : 0.6175003 34.87450 51.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1495962 -3.6416261E-03 midg,1,midg; midg,igrid,midg 5.0464712E-02 0.1084967 1,midg,midg; igrid,midg,midg 0.1588309 -0.1303065 gauss-seidel spectral radius is 0.9992477 estimated iterations to convergence 288 setup time was (sec) 1.850000 now iterating at: 23:47:06 rms-change max change #iterations 10.24650 331.4731 at 10iterations 6.045244 161.4129 at 20iterations 3.534685 81.97290 at 30iterations 2.057609 43.54016 at 40iterations 1.192766 22.78438 at 50iterations 0.6885273 14.81743 at 60iterations 0.3988037 7.594490 at 70iterations 0.2299241 4.489383 at 80iterations 0.1321734 2.758293 at 90iterations 7.6077960E-02 1.379767 at 100iterations 4.3640342E-02 1.039345 at 110iterations 2.5032001E-02 0.4520540 at 120iterations 1.4363659E-02 0.2722828 at 130iterations 8.2595572E-03 0.1722438 at 140iterations 4.7300509E-03 8.6788177E-02 at 150iterations 2.7063030E-03 5.6722641E-02 at 160iterations 1.5490489E-03 2.8543472E-02 at 170iterations 8.8705035E-04 1.6305685E-02 at 180iterations finished qdiffx linear iterations at : 23:47:16 total time elapsed so far: 11.97000 # loops : 180 mean,max change (kT/e) : 8.8705035E-04 1.6305685E-02 energy calculations done at 11.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 23:47:17 12.181u 0.187s 0:12.64 97.7% 0+0k 0+0io 0pf+0w