Sun Oct 9 17:26:11 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 17:26:11 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5608772 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): 3.450000 64.94500 ymin,ymax (A): 1.771000 61.82200 zmin,zma (A): -0.8310000 62.64100 x,y,z range (A): 61.49500 60.05100 63.47200 scale (grids/A): 0.5608772 object centre (A): 34.19750 31.79650 30.90500 number of atom coordinates read : 3656 total number of charged atoms : 3521 net assigned charge : -0.3789710 assigned positive charge : 553.0143 centred at (gu) : 89.64352 88.08469 88.48029 assigned negative charge : -553.3954 centred at (gu) : 89.57803 88.18770 88.38937 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7767 nv = 96 ne = 84 npr = 70443 no. pairs analyzed = 70443 no. exposed pairs = 4961 no. arc points = 34301 no. surface atoms = 1663 nbur = 1993 mkacc time = 0.1700000 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= 369 mr = 3967 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3528 ## 431 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9589237E-09 8.4554302E-10 midg,1,midg; midg,igrid,midg 2.2410038E-09 -9.5423980E-10 1,midg,midg; igrid,midg,midg -1.0676687E-09 7.9924073E-10 gauss-seidel spectral radius is 0.9836643 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 17:26:12 rms-change max change #iterations 9.2762031E-02 16.45028 at 10iterations 7.1701878E-03 0.9571838 at 20iterations 1.4174102E-03 0.1728935 at 30iterations 8.3071226E-04 9.5090151E-02 at 40iterations 5.1984860E-04 6.0171127E-02 at 50iterations finished qdiffx linear iterations at : 17:26:15 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.1984860E-04 6.0171127E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:26:15 3.403u 0.148s 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 17:26:15 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.682632 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): 3.450000 64.94500 ymin,ymax (A): 1.771000 61.82200 zmin,zma (A): -0.8310000 62.64100 x,y,z range (A): 61.49500 60.05100 63.47200 scale (grids/A): 1.682632 object centre (A): 34.19750 31.79650 30.90500 number of atom coordinates read : 3656 total number of charged atoms : 3521 net assigned charge : -0.3789710 assigned positive charge : 553.0143 centred at (gu) : 88.92948 84.25286 85.43934 assigned negative charge : -553.3954 centred at (gu) : 88.73370 84.56280 85.16778 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34301 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29329 mr = 58259 m= 3830 mr = 20055 m= 135 mr = 1927 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 38573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 325 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 27126 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) : 0.5608772 object centre at (A) : 34.19750 31.79650 30.90500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3210771E-02 -1.0082872E-02 midg,1,midg; midg,igrid,midg 1.4083824E-02 -6.4913034E-03 1,midg,midg; igrid,midg,midg 4.4696433E-03 1.2162368E-02 gauss-seidel spectral radius is 0.9983742 estimated iterations to convergence 197 setup time was (sec) 0.9200000 now iterating at: 17:26:16 rms-change max change #iterations 4.058957 186.1449 at 10iterations 1.774625 62.80140 at 20iterations 0.7776505 29.63466 at 30iterations 0.3402795 10.68799 at 40iterations 0.1490500 4.965613 at 50iterations 6.5432385E-02 2.102811 at 60iterations 2.8870663E-02 1.026703 at 70iterations 1.2794745E-02 0.3892097 at 80iterations 5.9214723E-03 0.1995544 at 90iterations 3.0683002E-03 9.9205971E-02 at 100iterations 1.9263495E-03 5.7353973E-02 at 110iterations 1.4589074E-03 4.2221069E-02 at 120iterations finished qdiffx linear iterations at : 17:26:23 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 1.4589074E-03 4.2221069E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 17:26:23 7.594u 0.183s 0:08.12 95.6% 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 17:26:24 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.523947 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): 3.450000 64.94500 ymin,ymax (A): 1.771000 61.82200 zmin,zma (A): -0.8310000 62.64100 x,y,z range (A): 61.49500 60.05100 63.47200 scale (grids/A): 2.523947 object centre (A): 34.19750 31.79650 30.90500 number of atom coordinates read : 3656 total number of charged atoms : 3521 net assigned charge : -0.3789710 assigned positive charge : 553.0143 centred at (gu) : 88.39392 81.37901 83.15859 assigned negative charge : -553.3954 centred at (gu) : 88.10039 81.84410 82.75168 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 198163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34301 grid for indexing accessible points = 1.400000 m= 97453 mr = 142451 m= 31782 mr = 76691 m= 6295 mr = 23670 m= 528 mr = 4115 m= 10 mr = 237 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.570000 number of dielectric boundary points 87068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 28145 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) : 1.682632 object centre at (A) : 34.19750 31.79650 30.90500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7772274 -0.1754974 midg,1,midg; midg,igrid,midg 0.1894950 -8.8263877E-02 1,midg,midg; igrid,midg,midg 0.1189444 6.4310268E-02 gauss-seidel spectral radius is 0.9992210 estimated iterations to convergence 283 setup time was (sec) 1.870000 now iterating at: 17:26:26 rms-change max change #iterations 10.59048 399.6274 at 10iterations 6.283972 171.8632 at 20iterations 3.685763 80.49356 at 30iterations 2.140657 51.56952 at 40iterations 1.242606 27.12774 at 50iterations 0.7166969 14.45673 at 60iterations 0.4128011 8.243149 at 70iterations 0.2366351 4.959656 at 80iterations 0.1356394 3.010876 at 90iterations 7.7589057E-02 1.536835 at 100iterations 4.4326998E-02 0.8742476 at 110iterations 2.5254929E-02 0.5044136 at 120iterations 1.4411335E-02 0.2856043 at 130iterations 8.2133319E-03 0.1545982 at 140iterations 4.6716835E-03 8.7164581E-02 at 150iterations 2.6572065E-03 4.7548771E-02 at 160iterations 1.5160738E-03 2.9783010E-02 at 170iterations 8.6459005E-04 1.5481949E-02 at 180iterations finished qdiffx linear iterations at : 17:26:36 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 8.6459005E-04 1.5481949E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 17:26:37 12.469u 0.199s 0:12.99 97.3% 0+0k 0+0io 0pf+0w