Sun Oct 9 12:47:59 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 12:47:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6990260 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): -6.657000 44.27100 ymin,ymax (A): -14.06500 36.16900 zmin,zma (A): 2.277000 44.74500 x,y,z range (A): 50.92800 50.23400 42.46800 scale (grids/A): 0.6990260 object centre (A): 18.80700 11.05200 23.51100 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500012 assigned positive charge : 359.9890 centred at (gu) : 89.64602 91.35788 90.63572 assigned negative charge : -356.4896 centred at (gu) : 89.68241 91.52698 90.67606 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7826 nv = 96 ne = 84 npr = 47599 no. pairs analyzed = 47599 no. exposed pairs = 3028 no. arc points = 20781 no. surface atoms = 1022 nbur = 1344 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4343 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2011 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9024865E-08 7.2654673E-09 midg,1,midg; midg,igrid,midg 7.8729840E-08 -7.2690952E-08 1,midg,midg; igrid,midg,midg 4.5373493E-08 7.9375271E-09 gauss-seidel spectral radius is 0.9893644 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 12:48:00 rms-change max change #iterations 0.2005092 29.22429 at 10iterations 2.4433844E-02 3.333435 at 20iterations 3.3426997E-03 0.4704895 at 30iterations 6.5292011E-04 9.5062256E-02 at 40iterations 1.9463545E-04 2.7593613E-02 at 50iterations finished qdiffx linear iterations at : 12:48:03 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.9463545E-04 2.7593613E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 12:48:03 3.361u 0.187s 0:03.86 91.7% 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 12:48:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.097078 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): -6.657000 44.27100 ymin,ymax (A): -14.06500 36.16900 zmin,zma (A): 2.277000 44.74500 x,y,z range (A): 50.92800 50.23400 42.46800 scale (grids/A): 2.097078 object centre (A): 18.80700 11.05200 23.51100 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500012 assigned positive charge : 359.9890 centred at (gu) : 88.93752 94.07311 91.90678 assigned negative charge : -356.4896 centred at (gu) : 89.04681 94.58068 92.02796 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20781 grid for indexing accessible points = 1.400000 m= 32275 mr = 57160 m= 6018 mr = 23925 m= 612 mr = 3925 m= 18 mr = 312 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 35952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17673 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) : 0.6990260 object centre at (A) : 18.80700 11.05200 23.51100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9739845E-02 8.3251679E-03 midg,1,midg; midg,igrid,midg 1.8982697E-02 -4.5519330E-02 1,midg,midg; igrid,midg,midg 6.3298181E-02 -1.6705489E-02 gauss-seidel spectral radius is 0.9988411 estimated iterations to convergence 233 setup time was (sec) 0.6300000 now iterating at: 12:48:04 rms-change max change #iterations 4.854540 201.0506 at 10iterations 2.410882 85.45599 at 20iterations 1.195438 38.98685 at 30iterations 0.5941087 20.09966 at 40iterations 0.2950566 9.460711 at 50iterations 0.1472395 4.159541 at 60iterations 7.3346056E-02 2.008364 at 70iterations 3.6581464E-02 1.100555 at 80iterations 1.8351132E-02 0.5146103 at 90iterations 9.2649180E-03 0.2658558 at 100iterations 4.7456501E-03 0.1377354 at 110iterations 2.4991003E-03 8.0444336E-02 at 120iterations finished qdiffx linear iterations at : 12:48:11 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.4991003E-03 8.0444336E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 12:48:12 7.841u 0.213s 0:08.33 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 12:48:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.145617 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): -6.657000 44.27100 ymin,ymax (A): -14.06500 36.16900 zmin,zma (A): 2.277000 44.74500 x,y,z range (A): 50.92800 50.23400 42.46800 scale (grids/A): 3.145617 object centre (A): 18.80700 11.05200 23.51100 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500012 assigned positive charge : 359.9890 centred at (gu) : 88.40610 96.10957 92.86003 assigned negative charge : -356.4896 centred at (gu) : 88.57017 96.87103 93.04178 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 190015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20781 grid for indexing accessible points = 1.400000 m= 100668 mr = 138063 m= 40185 mr = 82549 m= 11233 mr = 32526 m= 2272 mr = 8520 m= 310 mr = 1650 m= 13 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 81167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17796 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) : 2.097078 object centre at (A) : 18.80700 11.05200 23.51100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4723806 -1.0227067E-02 midg,1,midg; midg,igrid,midg 0.3159180 -0.4543013 1,midg,midg; igrid,midg,midg 0.6853159 -0.4592882 gauss-seidel spectral radius is 0.9993029 estimated iterations to convergence 299 setup time was (sec) 1.510000 now iterating at: 12:48:13 rms-change max change #iterations 10.93680 449.6384 at 10iterations 6.497336 142.0814 at 20iterations 3.849026 74.06923 at 30iterations 2.280282 41.42290 at 40iterations 1.348173 24.37357 at 50iterations 0.7963334 13.82450 at 60iterations 0.4690588 7.937309 at 70iterations 0.2758845 4.948915 at 80iterations 0.1620997 2.774801 at 90iterations 9.5139638E-02 1.553360 at 100iterations 5.5977050E-02 0.9491768 at 110iterations 3.2914501E-02 0.6177256 at 120iterations 1.9464875E-02 0.3230591 at 130iterations 1.1626329E-02 0.2012711 at 140iterations 7.0447735E-03 0.1270294 at 150iterations 4.4040717E-03 8.3747864E-02 at 160iterations 2.8762014E-03 6.0161591E-02 at 170iterations 2.0046537E-03 4.2037964E-02 at 180iterations finished qdiffx linear iterations at : 12:48:25 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 2.0046537E-03 4.2037964E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.12000 DelPhi exited at 12:48:25 13.119u 0.197s 0:13.57 98.0% 0+0k 0+0io 0pf+0w