Sat Oct 8 14:13:23 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 Sat Oct 8 2011 at 14:13:23 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6183884 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): -11.42000 43.21400 ymin,ymax (A): 9.849999 55.21300 zmin,zma (A): 36.50100 94.07000 x,y,z range (A): 54.63400 45.36300 57.56900 scale (grids/A): 0.6183884 object centre (A): 15.89700 32.53150 65.28550 number of atom coordinates read : 2952 total number of charged atoms : 2805 net assigned charge : -1.999993 assigned positive charge : 441.7837 centred at (gu) : 89.17136 89.84605 91.37059 assigned negative charge : -443.7844 centred at (gu) : 89.11334 89.74569 91.34235 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7552 nv = 96 ne = 84 npr = 60951 no. pairs analyzed = 60951 no. exposed pairs = 3438 no. arc points = 23654 no. surface atoms = 1170 nbur = 1782 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 4391 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2371 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6343250E-09 7.6130358E-10 midg,1,midg; midg,igrid,midg -9.1559142E-09 5.4800147E-09 1,midg,midg; igrid,midg,midg -6.8914114E-09 2.2025790E-09 gauss-seidel spectral radius is 0.9864854 estimated iterations to convergence 70 setup time was (sec) 0.8600000 now iterating at: 14:13:25 rms-change max change #iterations 0.1382375 23.05861 at 10iterations 1.3247120E-02 1.737221 at 20iterations 1.4021250E-03 0.2227039 at 30iterations 2.0614073E-04 2.8894424E-02 at 40iterations 4.2239735E-05 6.4907074E-03 at 50iterations finished qdiffx linear iterations at : 14:13:32 total time elapsed so far: 8.060000 # loops : 50 mean,max change (kT/e) : 4.2239735E-05 6.4907074E-03 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 14:13:33 8.245u 0.707s 0:09.29 96.2% 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 Sat Oct 8 2011 at 14:13:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.855165 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): -11.42000 43.21400 ymin,ymax (A): 9.849999 55.21300 zmin,zma (A): 36.50100 94.07000 x,y,z range (A): 54.63400 45.36300 57.56900 scale (grids/A): 1.855165 object centre (A): 15.89700 32.53150 65.28550 number of atom coordinates read : 2952 total number of charged atoms : 2805 net assigned charge : -1.999993 assigned positive charge : 441.7837 centred at (gu) : 87.51350 89.53741 94.11154 assigned negative charge : -443.7844 centred at (gu) : 87.34005 89.23666 94.02681 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83207 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23654 grid for indexing accessible points = 1.400000 m= 30559 mr = 60328 m= 4555 mr = 23181 m= 216 mr = 2776 m= 0 mr = 56 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.6900000 number of dielectric boundary points 32196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 22001 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) : 0.6183884 object centre at (A) : 15.89700 32.53150 65.28550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1363915E-02 5.4648775E-03 midg,1,midg; midg,igrid,midg -2.7873127E-03 1.4102485E-02 1,midg,midg; igrid,midg,midg -4.4768922E-02 2.1324332E-03 gauss-seidel spectral radius is 0.9985970 estimated iterations to convergence 212 setup time was (sec) 1.010000 now iterating at: 14:13:34 rms-change max change #iterations 4.401134 179.1036 at 10iterations 2.033627 62.34084 at 20iterations 0.9475425 30.10181 at 30iterations 0.4386111 16.00250 at 40iterations 0.2041557 7.450836 at 50iterations 9.4947763E-02 3.030029 at 60iterations 4.3985005E-02 1.272695 at 70iterations 2.0403752E-02 0.6313591 at 80iterations 9.5176203E-03 0.2874131 at 90iterations 4.4487840E-03 0.1370430 at 100iterations 2.0827707E-03 6.0436249E-02 at 110iterations 9.7725203E-04 2.9005051E-02 at 120iterations finished qdiffx linear iterations at : 14:13:51 total time elapsed so far: 18.23000 # loops : 120 mean,max change (kT/e) : 9.7725203E-04 2.9005051E-02 energy calculations done at 18.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.40000 DelPhi exited at 14:13:52 18.403u 0.645s 0:19.37 98.2% 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 Sat Oct 8 2011 at 14:13:52 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.782748 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): -11.42000 43.21400 ymin,ymax (A): 9.849999 55.21300 zmin,zma (A): 36.50100 94.07000 x,y,z range (A): 54.63400 45.36300 57.56900 scale (grids/A): 2.782748 object centre (A): 15.89700 32.53150 65.28550 number of atom coordinates read : 2952 total number of charged atoms : 2805 net assigned charge : -1.999993 assigned positive charge : 441.7837 centred at (gu) : 86.27011 89.30607 96.16724 assigned negative charge : -443.7844 centred at (gu) : 86.00980 88.85504 96.04005 start vw surface at 0.1400000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 192759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23654 grid for indexing accessible points = 1.400000 m= 99832 mr = 145516 m= 35527 mr = 83602 m= 8022 mr = 28911 m= 1013 mr = 5935 m= 37 mr = 671 m= 0 mr = 9 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 452 time to turn everything in is 2.110000 number of dielectric boundary points 72546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 22439 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) : 1.855165 object centre at (A) : 15.89700 32.53150 65.28550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0658193E-02 0.1041408 midg,1,midg; midg,igrid,midg -1.5176491E-02 0.1642600 1,midg,midg; igrid,midg,midg -0.5485746 0.1528828 gauss-seidel spectral radius is 0.9992518 estimated iterations to convergence 289 setup time was (sec) 2.770000 now iterating at: 14:13:56 rms-change max change #iterations 10.31465 322.7390 at 10iterations 6.040529 132.4296 at 20iterations 3.493484 75.97098 at 30iterations 2.025614 40.06625 at 40iterations 1.172935 22.71428 at 50iterations 0.6759145 13.76185 at 60iterations 0.3878070 6.972990 at 70iterations 0.2233113 4.156179 at 80iterations 0.1281686 2.313177 at 90iterations 7.3760360E-02 1.388060 at 100iterations 4.2305514E-02 0.7490377 at 110iterations 2.4344407E-02 0.4108696 at 120iterations 1.3952715E-02 0.2655563 at 130iterations 8.0253873E-03 0.1427334 at 140iterations 4.6246545E-03 8.0383301E-02 at 150iterations 2.6711875E-03 4.5066833E-02 at 160iterations 1.5490435E-03 2.7908325E-02 at 170iterations 9.0684259E-04 1.6616821E-02 at 180iterations finished qdiffx linear iterations at : 14:14:23 total time elapsed so far: 30.13000 # loops : 180 mean,max change (kT/e) : 9.0684259E-04 1.6616821E-02 energy calculations done at 30.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.30000 DelPhi exited at 14:14:24 30.307u 0.861s 0:31.49 98.9% 0+0k 0+0io 0pf+0w