Sun Oct 9 01:49:41 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 01:49:41 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6638942 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): -27.12000 26.50300 ymin,ymax (A): 8.695000 52.62100 zmin,zma (A): -11.67000 41.78600 x,y,z range (A): 53.62300 43.92600 53.45600 scale (grids/A): 0.6638942 object centre (A): -0.3085003 30.65800 15.05800 number of atom coordinates read : 2318 total number of charged atoms : 2183 net assigned charge : 10.51402 assigned positive charge : 339.2845 centred at (gu) : 90.52441 90.84151 91.14423 assigned negative charge : -328.7711 centred at (gu) : 90.56668 90.72448 91.11169 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7090 nv = 96 ne = 84 npr = 46372 no. pairs analyzed = 46372 no. exposed pairs = 3104 no. arc points = 22822 no. surface atoms = 1022 nbur = 1296 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 420 mr = 3672 m= 0 mr = 47 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3100000 number of dielectric boundary points 3791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8692347E-08 4.4630987E-08 midg,1,midg; midg,igrid,midg 6.5367982E-09 6.0332056E-08 1,midg,midg; igrid,midg,midg 3.3449563E-08 2.3880792E-08 gauss-seidel spectral radius is 0.9882247 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 01:49:42 rms-change max change #iterations 0.1593306 26.30072 at 10iterations 1.7080706E-02 2.684735 at 20iterations 1.8163658E-03 0.2497177 at 30iterations 2.0475651E-04 3.2997131E-02 at 40iterations 2.4112383E-05 3.3435822E-03 at 50iterations finished qdiffx linear iterations at : 01:49:45 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 2.4112383E-05 3.3435822E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.010000 DelPhi exited at 01:49:46 4.017u 0.280s 0:04.56 94.0% 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 01:49:46 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991683 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): -27.12000 26.50300 ymin,ymax (A): 8.695000 52.62100 zmin,zma (A): -11.67000 41.78600 x,y,z range (A): 53.62300 43.92600 53.45600 scale (grids/A): 1.991683 object centre (A): -0.3085003 30.65800 15.05800 number of atom coordinates read : 2318 total number of charged atoms : 2183 net assigned charge : 10.51402 assigned positive charge : 339.2845 centred at (gu) : 91.57268 92.52428 93.43226 assigned negative charge : -328.7711 centred at (gu) : 91.70028 92.17348 93.33503 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22822 grid for indexing accessible points = 1.400000 m= 27983 mr = 50254 m= 5103 mr = 20136 m= 428 mr = 3270 m= 14 mr = 177 m= 0 mr = 3 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 34933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 17281 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) : 0.6638942 object centre at (A) : -0.3085003 30.65800 15.05800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8824012E-02 3.6975082E-02 midg,1,midg; midg,igrid,midg -1.2168094E-02 3.3598959E-02 1,midg,midg; igrid,midg,midg 6.0292765E-02 7.1553208E-02 gauss-seidel spectral radius is 0.9987323 estimated iterations to convergence 222 setup time was (sec) 0.9800000 now iterating at: 01:49:47 rms-change max change #iterations 4.234641 181.1286 at 10iterations 2.039741 76.97980 at 20iterations 0.9749112 31.88063 at 30iterations 0.4696098 16.43442 at 40iterations 0.2249668 7.520385 at 50iterations 0.1080904 3.804090 at 60iterations 5.1995762E-02 1.576343 at 70iterations 2.5024727E-02 0.7815323 at 80iterations 1.2028348E-02 0.4027812 at 90iterations 5.7972902E-03 0.1822853 at 100iterations 2.7900469E-03 8.5367918E-02 at 110iterations 1.3412688E-03 4.0795326E-02 at 120iterations finished qdiffx linear iterations at : 01:49:55 total time elapsed so far: 9.260000 # loops : 120 mean,max change (kT/e) : 1.3412688E-03 4.0795326E-02 energy calculations done at 9.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.430000 DelPhi exited at 01:49:56 9.437u 0.297s 0:09.99 97.2% 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 Sun Oct 9 2011 at 01:49:56 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.987524 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): -27.12000 26.50300 ymin,ymax (A): 8.695000 52.62100 zmin,zma (A): -11.67000 41.78600 x,y,z range (A): 53.62300 43.92600 53.45600 scale (grids/A): 2.987524 object centre (A): -0.3085003 30.65800 15.05800 number of atom coordinates read : 2318 total number of charged atoms : 2183 net assigned charge : 10.51402 assigned positive charge : 339.2845 centred at (gu) : 92.35899 93.78648 95.14845 assigned negative charge : -328.7711 centred at (gu) : 92.55042 93.26020 95.00254 start vw surface at 0.1400000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 173517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22822 grid for indexing accessible points = 1.400000 m= 87979 mr = 121885 m= 33957 mr = 70557 m= 9505 mr = 27082 m= 1747 mr = 7266 m= 206 mr = 1196 m= 17 mr = 121 m= 0 mr = 9 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 78812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 17464 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) : 1.991683 object centre at (A) : -0.3085003 30.65800 15.05800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6488353 0.3775539 midg,1,midg; midg,igrid,midg -0.1368619 0.2993504 1,midg,midg; igrid,midg,midg 0.5637437 0.6349148 gauss-seidel spectral radius is 0.9992974 estimated iterations to convergence 298 setup time was (sec) 2.100000 now iterating at: 01:49:58 rms-change max change #iterations 9.977752 416.2339 at 10iterations 5.921739 137.5926 at 20iterations 3.503231 76.57687 at 30iterations 2.065248 38.86044 at 40iterations 1.213537 22.99759 at 50iterations 0.7135220 15.33094 at 60iterations 0.4178056 7.659704 at 70iterations 0.2440476 4.313410 at 80iterations 0.1429069 2.600608 at 90iterations 8.3413698E-02 1.563737 at 100iterations 4.8768409E-02 0.9334307 at 110iterations 2.8493561E-02 0.6065407 at 120iterations 1.6628535E-02 0.3022461 at 130iterations 9.7028129E-03 0.1916351 at 140iterations 5.6563555E-03 9.9178314E-02 at 150iterations 3.3072492E-03 6.1096191E-02 at 160iterations 1.9325520E-03 3.5864830E-02 at 170iterations 1.1323916E-03 2.0649910E-02 at 180iterations finished qdiffx linear iterations at : 01:50:12 total time elapsed so far: 15.79000 # loops : 180 mean,max change (kT/e) : 1.1323916E-03 2.0649910E-02 energy calculations done at 15.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.96000 DelPhi exited at 01:50:13 15.963u 0.306s 0:16.58 98.0% 0+0k 0+0io 0pf+0w