Tue Oct 11 06:01:51 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 Tue Oct 11 2011 at 06:01:51 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7066437 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): 25.62900 71.97900 ymin,ymax (A): -18.78300 31.59600 zmin,zma (A): 3.948000 46.28300 x,y,z range (A): 46.35000 50.37900 42.33500 scale (grids/A): 0.7066437 object centre (A): 48.80400 6.406501 25.11550 number of atom coordinates read : 2318 total number of charged atoms : 1992 net assigned charge : 6.039011 assigned positive charge : 326.5359 centred at (gu) : 89.21513 90.15663 90.39483 assigned negative charge : -320.4970 centred at (gu) : 89.34216 90.09253 90.47594 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7203 nv = 96 ne = 84 npr = 42545 no. pairs analyzed = 42545 no. exposed pairs = 2573 no. arc points = 17500 no. surface atoms = 875 nbur = 1443 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 497 mr = 4221 m= 4 mr = 96 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1602 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7972 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3178442E-08 9.2842249E-09 midg,1,midg; midg,igrid,midg 1.6982646E-08 8.3889510E-08 1,midg,midg; igrid,midg,midg 1.3080216E-07 -1.2058381E-08 gauss-seidel spectral radius is 0.9895637 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 06:01:52 rms-change max change #iterations 0.2043777 29.20546 at 10iterations 2.5948668E-02 3.199986 at 20iterations 3.4624818E-03 0.4296646 at 30iterations 6.0506561E-04 7.5134277E-02 at 40iterations 1.6076714E-04 1.8369675E-02 at 50iterations finished qdiffx linear iterations at : 06:01:55 total time elapsed so far: 4.260000 # loops : 50 mean,max change (kT/e) : 1.6076714E-04 1.8369675E-02 energy calculations done at 4.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 06:01:56 4.426u 0.399s 0:05.12 93.9% 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 Tue Oct 11 2011 at 06:01:56 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.119931 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): 25.62900 71.97900 ymin,ymax (A): -18.78300 31.59600 zmin,zma (A): 3.948000 46.28300 x,y,z range (A): 46.35000 50.37900 42.33500 scale (grids/A): 2.119931 object centre (A): 48.80400 6.406501 25.11550 number of atom coordinates read : 2318 total number of charged atoms : 1992 net assigned charge : 6.039011 assigned positive charge : 326.5359 centred at (gu) : 87.64537 90.46986 91.18456 assigned negative charge : -320.4970 centred at (gu) : 88.02637 90.27765 91.42795 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17500 grid for indexing accessible points = 1.400000 m= 31468 mr = 54555 m= 6071 mr = 24181 m= 600 mr = 4149 m= 20 mr = 331 m= 0 mr = 6 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 31133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15813 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) : 0.7066437 object centre at (A) : 48.80400 6.406501 25.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9580590E-02 2.7256994E-02 midg,1,midg; midg,igrid,midg 3.8217749E-02 2.6402131E-02 1,midg,midg; igrid,midg,midg 4.4464748E-02 -4.6956003E-02 gauss-seidel spectral radius is 0.9988312 estimated iterations to convergence 232 setup time was (sec) 0.9500000 now iterating at: 06:01:57 rms-change max change #iterations 4.672871 224.1712 at 10iterations 2.311616 80.16763 at 20iterations 1.146847 37.56480 at 30iterations 0.5694157 16.52131 at 40iterations 0.2839934 11.35277 at 50iterations 0.1407291 4.491928 at 60iterations 6.9973901E-02 2.098754 at 70iterations 3.4794856E-02 1.226540 at 80iterations 1.7450936E-02 0.4813447 at 90iterations 8.7452000E-03 0.2591819 at 100iterations 4.4069383E-03 0.1315050 at 110iterations 2.2808139E-03 7.0627213E-02 at 120iterations finished qdiffx linear iterations at : 06:02:07 total time elapsed so far: 10.61000 # loops : 120 mean,max change (kT/e) : 2.2808139E-03 7.0627213E-02 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 06:02:08 10.776u 0.447s 0:12.53 89.4% 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 Tue Oct 11 2011 at 06:02:08 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: 335 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.179897 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): 25.62900 71.97900 ymin,ymax (A): -18.78300 31.59600 zmin,zma (A): 3.948000 46.28300 x,y,z range (A): 46.35000 50.37900 42.33500 scale (grids/A): 3.179897 object centre (A): 48.80400 6.406501 25.11550 number of atom coordinates read : 2318 total number of charged atoms : 1992 net assigned charge : 6.039011 assigned positive charge : 326.5359 centred at (gu) : 86.46800 90.70492 91.77674 assigned negative charge : -320.4970 centred at (gu) : 87.03960 90.41656 92.14198 start vw surface at 0.1200000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 175769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17500 grid for indexing accessible points = 1.400000 m= 97540 mr = 131422 m= 39893 mr = 81736 m= 11579 mr = 33066 m= 2396 mr = 9164 m= 324 mr = 1733 m= 29 mr = 221 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 70172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.150000 number of grid points assigned charge 15936 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) : 2.119931 object centre at (A) : 48.80400 6.406501 25.11550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1137501 0.2351450 midg,1,midg; midg,igrid,midg 0.2720285 0.1072198 1,midg,midg; igrid,midg,midg 0.4445167 -0.5830821 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 297 setup time was (sec) 2.360000 now iterating at: 06:02:11 rms-change max change #iterations 10.38932 325.7182 at 10iterations 6.146272 139.9436 at 20iterations 3.640035 122.6635 at 30iterations 2.146893 41.72322 at 40iterations 1.264876 29.22546 at 50iterations 0.7431597 17.12196 at 60iterations 0.4360258 8.018357 at 70iterations 0.2563719 4.778858 at 80iterations 0.1504093 2.574325 at 90iterations 8.8279583E-02 1.660324 at 100iterations 5.1874097E-02 0.8987751 at 110iterations 3.0568756E-02 0.5443268 at 120iterations 1.8190131E-02 0.3358269 at 130iterations 1.0966300E-02 0.2034836 at 140iterations 6.7717168E-03 0.1580982 at 150iterations 4.3131094E-03 0.1021271 at 160iterations 2.8957108E-03 5.6610107E-02 at 170iterations 2.0490841E-03 4.0325165E-02 at 180iterations finished qdiffx linear iterations at : 06:02:27 total time elapsed so far: 18.28000 # loops : 180 mean,max change (kT/e) : 2.0490841E-03 4.0325165E-02 energy calculations done at 18.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.45000 DelPhi exited at 06:02:28 18.454u 0.432s 0:19.19 98.3% 0+0k 0+0io 0pf+0w