Sun Oct 9 21:10:30 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 21:10:30 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6432960 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): 10.34100 65.68100 ymin,ymax (A): -11.99400 38.31700 zmin,zma (A): -11.64900 41.70200 x,y,z range (A): 55.34000 50.31100 53.35100 scale (grids/A): 0.6432960 object centre (A): 38.01100 13.16150 15.02650 number of atom coordinates read : 2587 total number of charged atoms : 2443 net assigned charge : 6.000012 assigned positive charge : 390.2548 centred at (gu) : 90.56902 90.75251 90.07119 assigned negative charge : -384.2556 centred at (gu) : 90.61495 90.70571 90.04129 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7073 nv = 96 ne = 84 npr = 52178 no. pairs analyzed = 52178 no. exposed pairs = 3083 no. arc points = 22158 no. surface atoms = 1039 nbur = 1548 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 362 mr = 3868 m= 0 mr = 41 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.1900000 number of dielectric boundary points 3526 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2184 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8503 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7115801E-09 1.3541237E-08 midg,1,midg; midg,igrid,midg 3.1666154E-09 1.8116245E-08 1,midg,midg; igrid,midg,midg 1.3627292E-08 4.1729309E-09 gauss-seidel spectral radius is 0.9874786 estimated iterations to convergence 73 setup time was (sec) 0.3800000 now iterating at: 21:10:31 rms-change max change #iterations 0.1498672 22.02612 at 10iterations 1.4989379E-02 2.284286 at 20iterations 1.5212280E-03 0.2131653 at 30iterations 1.4883911E-04 2.6599884E-02 at 40iterations 1.5484226E-05 2.3765564E-03 at 50iterations finished qdiffx linear iterations at : 21:10:34 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.5484226E-05 2.3765564E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 21:10:34 3.419u 0.189s 0:03.88 92.5% 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 21:10:34 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.929888 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): 10.34100 65.68100 ymin,ymax (A): -11.99400 38.31700 zmin,zma (A): -11.64900 41.70200 x,y,z range (A): 55.34000 50.31100 53.35100 scale (grids/A): 1.929888 object centre (A): 38.01100 13.16150 15.02650 number of atom coordinates read : 2587 total number of charged atoms : 2443 net assigned charge : 6.000012 assigned positive charge : 390.2548 centred at (gu) : 91.70651 92.25715 90.21308 assigned negative charge : -384.2556 centred at (gu) : 91.84456 92.11698 90.12365 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22158 grid for indexing accessible points = 1.400000 m= 25979 mr = 52939 m= 3905 mr = 18969 m= 231 mr = 2368 m= 0 mr = 104 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2099 time to turn everything in is 0.3800000 number of dielectric boundary points 32323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19247 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) : 0.6432960 object centre at (A) : 38.01100 13.16150 15.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4051087E-02 1.5812192E-02 midg,1,midg; midg,igrid,midg -1.7641006E-02 1.0220332E-02 1,midg,midg; igrid,midg,midg -9.5426459E-03 2.4928560E-02 gauss-seidel spectral radius is 0.9986625 estimated iterations to convergence 217 setup time was (sec) 0.5900000 now iterating at: 21:10:35 rms-change max change #iterations 4.298219 159.4308 at 10iterations 2.021831 65.71025 at 20iterations 0.9562299 29.70153 at 30iterations 0.4506661 13.85236 at 40iterations 0.2125414 7.343998 at 50iterations 0.1000460 3.137634 at 60iterations 4.7230061E-02 1.454122 at 70iterations 2.2303782E-02 0.6475277 at 80iterations 1.0495084E-02 0.3184175 at 90iterations 4.9487706E-03 0.1483221 at 100iterations 2.3439864E-03 8.0757141E-02 at 110iterations 1.1038159E-03 3.3188343E-02 at 120iterations finished qdiffx linear iterations at : 21:10:42 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.1038159E-03 3.3188343E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 21:10:43 7.896u 0.217s 0:08.44 95.9% 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 21:10:43 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 = 2587 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.894832 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): 10.34100 65.68100 ymin,ymax (A): -11.99400 38.31700 zmin,zma (A): -11.64900 41.70200 x,y,z range (A): 55.34000 50.31100 53.35100 scale (grids/A): 2.894832 object centre (A): 38.01100 13.16150 15.02650 number of atom coordinates read : 2587 total number of charged atoms : 2443 net assigned charge : 6.000012 assigned positive charge : 390.2548 centred at (gu) : 92.55959 93.38554 90.31954 assigned negative charge : -384.2556 centred at (gu) : 92.76672 93.17534 90.18551 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 177302 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22158 grid for indexing accessible points = 1.400000 m= 86186 mr = 128240 m= 29042 mr = 70575 m= 6819 mr = 22827 m= 1083 mr = 5031 m= 80 mr = 790 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 7053 time to turn everything in is 0.9700000 number of dielectric boundary points 73007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 19543 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) : 1.929888 object centre at (A) : 38.01100 13.16150 15.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3368594 -3.3100966E-02 midg,1,midg; midg,igrid,midg -0.2843180 0.1344990 1,midg,midg; igrid,midg,midg -4.9589254E-02 0.1836433 gauss-seidel spectral radius is 0.9992654 estimated iterations to convergence 291 setup time was (sec) 1.200000 now iterating at: 21:10:44 rms-change max change #iterations 10.00064 373.5802 at 10iterations 5.815537 135.2739 at 20iterations 3.366356 65.55352 at 30iterations 1.943878 38.98350 at 40iterations 1.119035 19.75261 at 50iterations 0.6463087 13.57330 at 60iterations 0.3722247 6.532579 at 70iterations 0.2141505 3.835546 at 80iterations 0.1231331 2.249452 at 90iterations 7.0842564E-02 1.161289 at 100iterations 4.0728003E-02 0.7274777 at 110iterations 2.3420040E-02 0.3973117 at 120iterations 1.3471712E-02 0.2252827 at 130iterations 7.7431798E-03 0.1373835 at 140iterations 4.4633695E-03 7.9097271E-02 at 150iterations 2.5635161E-03 4.5156837E-02 at 160iterations 1.4763967E-03 2.6046753E-02 at 170iterations 8.4900518E-04 1.5982725E-02 at 180iterations finished qdiffx linear iterations at : 21:10:55 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 8.4900518E-04 1.5982725E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 21:10:56 12.646u 0.202s 0:13.12 97.8% 0+0k 0+0io 0pf+0w