Sun Oct 9 21:53:46 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 21:53:47 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 = 3284 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: 0.5645506 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): -23.64600 39.41300 ymin,ymax (A): 6.700000 66.06100 zmin,zma (A): -27.68600 31.65000 x,y,z range (A): 63.05900 59.36100 59.33600 scale (grids/A): 0.5645506 object centre (A): 7.883501 36.38050 1.982000 number of atom coordinates read : 3284 total number of charged atoms : 3136 net assigned charge : 6.500022 assigned positive charge : 497.0985 centred at (gu) : 90.79277 89.73202 88.70803 assigned negative charge : -490.5999 centred at (gu) : 90.82050 89.77570 88.63495 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6931 nv = 96 ne = 84 npr = 63994 no. pairs analyzed = 63994 no. exposed pairs = 4470 no. arc points = 32673 no. surface atoms = 1476 nbur = 1808 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 = 1.540000 m= 296 mr = 3352 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3865 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3340 ## 460 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9009 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2338376E-10 1.3767729E-09 midg,1,midg; midg,igrid,midg 1.5514490E-09 1.9404700E-10 1,midg,midg; igrid,midg,midg 1.0199440E-09 5.1904614E-10 gauss-seidel spectral radius is 0.9838494 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 21:53:47 rms-change max change #iterations 8.9205660E-02 12.59812 at 10iterations 6.4228168E-03 1.275639 at 20iterations 4.7516954E-04 7.0312500E-02 at 30iterations 3.6648056E-05 5.5351257E-03 at 40iterations 4.6676892E-06 6.6745281E-04 at 50iterations finished qdiffx linear iterations at : 21:53:50 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 4.6676892E-06 6.6745281E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.150000 DelPhi exited at 21:53:50 3.151u 0.171s 0:03.69 89.9% 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 21:53:50 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 = 3284 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.693652 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): -23.64600 39.41300 ymin,ymax (A): 6.700000 66.06100 zmin,zma (A): -27.68600 31.65000 x,y,z range (A): 63.05900 59.36100 59.33600 scale (grids/A): 1.693652 object centre (A): 7.883501 36.38050 1.982000 number of atom coordinates read : 3284 total number of charged atoms : 3136 net assigned charge : 6.500022 assigned positive charge : 497.0985 centred at (gu) : 92.37743 89.19498 86.12331 assigned negative charge : -490.5999 centred at (gu) : 92.46124 89.32678 85.90453 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32673 grid for indexing accessible points = 1.400000 m= 22834 mr = 49238 m= 2651 mr = 15076 m= 95 mr = 1332 m= 0 mr = 15 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 361 time to turn everything in is 0.5200000 number of dielectric boundary points 35981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 24175 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) : 0.5645506 object centre at (A) : 7.883501 36.38050 1.982000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2618245E-02 1.4457392E-02 midg,1,midg; midg,igrid,midg 2.4547055E-03 -1.9610311E-04 1,midg,midg; igrid,midg,midg 8.9308843E-03 3.2689124E-02 gauss-seidel spectral radius is 0.9983705 estimated iterations to convergence 197 setup time was (sec) 0.7700000 now iterating at: 21:53:51 rms-change max change #iterations 3.772276 165.8891 at 10iterations 1.639243 56.21453 at 20iterations 0.7144811 25.08975 at 30iterations 0.3100081 10.83223 at 40iterations 0.1352728 4.464158 at 50iterations 5.8748495E-02 2.077351 at 60iterations 2.5596956E-02 0.8975387 at 70iterations 1.1159451E-02 0.3571491 at 80iterations 4.8670731E-03 0.1732202 at 90iterations 2.1221035E-03 7.0276260E-02 at 100iterations 9.2853396E-04 3.0582428E-02 at 110iterations 4.0650298E-04 1.5029907E-02 at 120iterations finished qdiffx linear iterations at : 21:53:57 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 4.0650298E-04 1.5029907E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 21:53:58 6.971u 0.170s 0:07.41 96.3% 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 Sun Oct 9 2011 at 21:53:58 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 = 3284 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: 2.540478 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): -23.64600 39.41300 ymin,ymax (A): 6.700000 66.06100 zmin,zma (A): -27.68600 31.65000 x,y,z range (A): 63.05900 59.36100 59.33600 scale (grids/A): 2.540478 object centre (A): 7.883501 36.38050 1.982000 number of atom coordinates read : 3284 total number of charged atoms : 3136 net assigned charge : 6.500022 assigned positive charge : 497.0985 centred at (gu) : 93.56597 88.79242 84.18469 assigned negative charge : -490.5999 centred at (gu) : 93.69160 88.99017 83.85669 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 176278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32673 grid for indexing accessible points = 1.400000 m= 78562 mr = 121005 m= 22753 mr = 60458 m= 4317 mr = 16515 m= 404 mr = 2879 m= 12 mr = 230 m= 0 mr = 4 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 1212 time to turn everything in is 1.210000 number of dielectric boundary points 81235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 25070 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) : 1.693652 object centre at (A) : 7.883501 36.38050 1.982000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3250929 0.2482190 midg,1,midg; midg,igrid,midg 4.9435232E-02 -8.1759341E-02 1,midg,midg; igrid,midg,midg 0.3728878 0.7847764 gauss-seidel spectral radius is 0.9992161 estimated iterations to convergence 282 setup time was (sec) 1.490000 now iterating at: 21:53:59 rms-change max change #iterations 9.750728 334.2694 at 10iterations 5.713922 153.8381 at 20iterations 3.314294 92.08610 at 30iterations 1.916503 49.41230 at 40iterations 1.101793 25.34929 at 50iterations 0.6330745 17.64322 at 60iterations 0.3622120 7.643402 at 70iterations 0.2065139 4.648943 at 80iterations 0.1174804 2.406256 at 90iterations 6.6990212E-02 1.416084 at 100iterations 3.8027279E-02 0.7325325 at 110iterations 2.1587424E-02 0.3888435 at 120iterations 1.2241513E-02 0.2409191 at 130iterations 6.9540623E-03 0.1406174 at 140iterations 3.9329743E-03 8.6750984E-02 at 150iterations 2.2296119E-03 4.3575287E-02 at 160iterations 1.2638483E-03 2.4856567E-02 at 170iterations 7.1533659E-04 1.2886047E-02 at 180iterations finished qdiffx linear iterations at : 21:54:09 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 7.1533659E-04 1.2886047E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.10000 DelPhi exited at 21:54:09 11.103u 0.160s 0:11.53 97.6% 0+0k 0+0io 0pf+0w