Sun Oct 9 09:00:36 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 09:00:36 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 = 5655 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: 0.5269234 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): 15.45500 83.01700 ymin,ymax (A): 17.86400 84.17400 zmin,zma (A): 1.166000 68.00400 x,y,z range (A): 67.56200 66.31001 66.83800 scale (grids/A): 0.5269234 object centre (A): 49.23600 51.01900 34.58500 number of atom coordinates read : 5655 total number of charged atoms : 5488 net assigned charge : -4.499979 assigned positive charge : 848.1605 centred at (gu) : 90.54067 89.11112 90.60506 assigned negative charge : -852.6676 centred at (gu) : 90.49796 89.14600 90.68816 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 10070 nv = 96 ne = 84 npr = 113777 no. pairs analyzed = 113777 no. exposed pairs = 7295 no. arc points = 49410 no. surface atoms = 2413 nbur = 3242 mkacc time = 0.2000000 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 = 1.596000 m= 355 mr = 5223 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3700000 number of dielectric boundary points 5190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4985 ## 682 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 13445 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1624089E-10 -7.4914364E-10 midg,1,midg; midg,igrid,midg 1.0499516E-10 -2.7328720E-10 1,midg,midg; igrid,midg,midg -3.4038614E-10 1.4956994E-10 gauss-seidel spectral radius is 0.9816449 estimated iterations to convergence 61 setup time was (sec) 0.5500000 now iterating at: 09:00:37 rms-change max change #iterations 8.4745124E-02 12.15431 at 10iterations 5.5132299E-03 0.7238035 at 20iterations 5.3081295E-04 0.1110916 at 30iterations 1.2366049E-04 3.0134201E-02 at 40iterations 3.7306370E-05 8.7661743E-03 at 50iterations finished qdiffx linear iterations at : 09:00:39 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.7306370E-05 8.7661743E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 09:00:40 3.524u 0.170s 0:04.01 92.0% 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 09:00:40 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 = 5655 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: 1.580770 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): 15.45500 83.01700 ymin,ymax (A): 17.86400 84.17400 zmin,zma (A): 1.166000 68.00400 x,y,z range (A): 67.56200 66.31001 66.83800 scale (grids/A): 1.580770 object centre (A): 49.23600 51.01900 34.58500 number of atom coordinates read : 5655 total number of charged atoms : 5488 net assigned charge : -4.499979 assigned positive charge : 848.1605 centred at (gu) : 91.62047 87.33141 91.81336 assigned negative charge : -852.6676 centred at (gu) : 91.49339 87.43764 92.06414 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 113047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49410 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 34046 mr = 77629 m= 2974 mr = 22720 m= 49 mr = 1333 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2139 time to turn everything in is 0.5400000 number of dielectric boundary points 48434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 618 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 41672 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) : 0.5269234 object centre at (A) : 49.23600 51.01900 34.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2053587E-02 -4.7864795E-02 midg,1,midg; midg,igrid,midg -8.1300251E-03 -2.0605940E-02 1,midg,midg; igrid,midg,midg 3.3924384E-03 -8.4734417E-04 gauss-seidel spectral radius is 0.9983274 estimated iterations to convergence 194 setup time was (sec) 0.7600000 now iterating at: 09:00:41 rms-change max change #iterations 4.523148 172.4903 at 10iterations 1.948340 59.40285 at 20iterations 0.8421407 25.26822 at 30iterations 0.3643910 11.92882 at 40iterations 0.1571991 4.428337 at 50iterations 6.8109855E-02 2.060097 at 60iterations 2.9548526E-02 0.7968831 at 70iterations 1.2819812E-02 0.3759420 at 80iterations 5.5525447E-03 0.1635704 at 90iterations 2.4182831E-03 6.8897247E-02 at 100iterations 1.0630407E-03 3.1167507E-02 at 110iterations 4.7291216E-04 1.4739990E-02 at 120iterations finished qdiffx linear iterations at : 09:00:48 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 4.7291216E-04 1.4739990E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 09:00:48 8.053u 0.199s 0:08.52 96.7% 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 09:00:49 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 = 5655 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: 2.371156 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): 15.45500 83.01700 ymin,ymax (A): 17.86400 84.17400 zmin,zma (A): 1.166000 68.00400 x,y,z range (A): 67.56200 66.31001 66.83800 scale (grids/A): 2.371156 object centre (A): 49.23600 51.01900 34.58500 number of atom coordinates read : 5655 total number of charged atoms : 5488 net assigned charge : -4.499979 assigned positive charge : 848.1605 centred at (gu) : 92.43031 85.99680 92.71960 assigned negative charge : -852.6676 centred at (gu) : 92.24010 86.15639 93.09612 start vw surface at 0.1400000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 262744 reading accessible surface arcs data from file ARCDAT no. of arc points read = 49410 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 120816 mr = 190276 m= 31708 mr = 94627 m= 4560 mr = 22949 m= 274 mr = 2874 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 7004 time to turn everything in is 1.330000 number of dielectric boundary points 109288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 43794 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) : 1.580770 object centre at (A) : 49.23600 51.01900 34.58500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1887903 -1.081643 midg,1,midg; midg,igrid,midg -0.1257193 -0.3659475 1,midg,midg; igrid,midg,midg 0.2937795 0.1169458 gauss-seidel spectral radius is 0.9992550 estimated iterations to convergence 289 setup time was (sec) 1.570000 now iterating at: 09:00:50 rms-change max change #iterations 12.00660 281.5914 at 10iterations 7.160899 184.1329 at 20iterations 4.245622 82.45983 at 30iterations 2.501729 57.80174 at 40iterations 1.465798 27.20626 at 50iterations 0.8571360 16.76348 at 60iterations 0.4991296 8.844901 at 70iterations 0.2907423 6.024428 at 80iterations 0.1687389 2.942798 at 90iterations 9.7875707E-02 1.779650 at 100iterations 5.6644782E-02 0.9902782 at 110iterations 3.2724287E-02 0.5682840 at 120iterations 1.8933678E-02 0.3407589 at 130iterations 1.0934322E-02 0.2030916 at 140iterations 6.3149831E-03 0.1098347 at 150iterations 3.6407195E-03 6.5437317E-02 at 160iterations 2.1002998E-03 3.4805298E-02 at 170iterations 1.2151370E-03 1.9653320E-02 at 180iterations finished qdiffx linear iterations at : 09:01:02 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 1.2151370E-03 1.9653320E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 09:01:03 13.644u 0.226s 0:14.21 97.5% 0+0k 0+0io 0pf+0w