Sun Oct 9 13:35:39 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 Sun Oct 9 2011 at 13:35:39 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2348 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7110330 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): -18.42600 30.23100 ymin,ymax (A): -20.54900 29.51900 zmin,zma (A): 4.554000 48.36100 x,y,z range (A): 48.65700 50.06800 43.80700 scale (grids/A): 0.7110330 object centre (A): 5.902501 4.485001 26.45750 number of atom coordinates read : 2348 total number of charged atoms : 2204 net assigned charge : 3.406011 assigned positive charge : 356.8553 centred at (gu) : 90.66581 90.30141 90.24184 assigned negative charge : -353.4496 centred at (gu) : 90.71008 90.46954 90.36823 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8131 nv = 96 ne = 84 npr = 47496 no. pairs analyzed = 47496 no. exposed pairs = 2932 no. arc points = 20406 no. surface atoms = 995 nbur = 1353 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4561 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4002 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1923 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8970 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0290039E-07 -4.7794614E-08 midg,1,midg; midg,igrid,midg 1.2487270E-07 -7.6074762E-08 1,midg,midg; igrid,midg,midg 5.1842779E-08 5.6583169E-09 gauss-seidel spectral radius is 0.9897202 estimated iterations to convergence 80 setup time was (sec) 0.5200000 now iterating at: 13:35:39 rms-change max change #iterations 0.2220178 27.31498 at 10iterations 2.7513273E-02 3.552952 at 20iterations 3.5843216E-03 0.4479294 at 30iterations 5.3343002E-04 6.6394806E-02 at 40iterations 1.0452777E-04 1.3607025E-02 at 50iterations finished qdiffx linear iterations at : 13:35:42 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.0452777E-04 1.3607025E-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) 3.380000 DelPhi exited at 13:35:42 3.379u 0.195s 0:03.84 92.7% 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 13:35:42 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2348 !!! WARNING: GLM 182 has a net charge of -0.0940 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: 2.133099 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): -18.42600 30.23100 ymin,ymax (A): -20.54900 29.51900 zmin,zma (A): 4.554000 48.36100 x,y,z range (A): 48.65700 50.06800 43.80700 scale (grids/A): 2.133099 object centre (A): 5.902501 4.485001 26.45750 number of atom coordinates read : 2348 total number of charged atoms : 2204 net assigned charge : 3.406011 assigned positive charge : 356.8553 centred at (gu) : 91.99690 90.90376 90.72514 assigned negative charge : -353.4496 centred at (gu) : 92.13015 91.40836 91.10443 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 86345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20406 grid for indexing accessible points = 1.400000 m= 33283 mr = 60210 m= 6317 mr = 25026 m= 624 mr = 4186 m= 17 mr = 324 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 282 time to turn everything in is 0.6000000 number of dielectric boundary points 36838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17529 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) : 0.7110330 object centre at (A) : 5.902501 4.485001 26.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2074475E-02 9.6395547E-03 midg,1,midg; midg,igrid,midg -1.3771794E-02 -0.1072146 1,midg,midg; igrid,midg,midg -4.8434488E-03 1.1977961E-02 gauss-seidel spectral radius is 0.9988766 estimated iterations to convergence 236 setup time was (sec) 0.8800000 now iterating at: 13:35:44 rms-change max change #iterations 5.017831 186.0644 at 10iterations 2.512329 81.38062 at 20iterations 1.261356 38.96255 at 30iterations 0.6349125 18.20564 at 40iterations 0.3188167 8.761934 at 50iterations 0.1600119 4.749643 at 60iterations 8.0750056E-02 2.199377 at 70iterations 4.0454742E-02 1.167572 at 80iterations 2.0438781E-02 0.6011931 at 90iterations 1.0321658E-02 0.3087473 at 100iterations 5.2206926E-03 0.1469193 at 110iterations 2.6482895E-03 7.4303627E-02 at 120iterations finished qdiffx linear iterations at : 13:35:50 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 2.6482895E-03 7.4303627E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 13:35:50 7.027u 0.239s 0:07.56 95.8% 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 13:35:50 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2348 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.199648 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): -18.42600 30.23100 ymin,ymax (A): -20.54900 29.51900 zmin,zma (A): 4.554000 48.36100 x,y,z range (A): 48.65700 50.06800 43.80700 scale (grids/A): 3.199648 object centre (A): 5.902501 4.485001 26.45750 number of atom coordinates read : 2348 total number of charged atoms : 2204 net assigned charge : 3.406011 assigned positive charge : 356.8553 centred at (gu) : 92.99531 91.35571 91.08758 assigned negative charge : -353.4496 centred at (gu) : 93.19508 92.11250 91.65662 start vw surface at 0.1700000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 199020 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20406 grid for indexing accessible points = 1.400000 m= 104697 mr = 145196 m= 41196 mr = 86489 m= 11837 mr = 33705 m= 2672 mr = 9183 m= 321 mr = 2034 m= 16 mr = 180 m= 0 mr = 3 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1047 time to turn everything in is 1.910000 number of dielectric boundary points 82969 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 17632 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) : 2.133099 object centre at (A) : 5.902501 4.485001 26.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5517623 4.3038666E-02 midg,1,midg; midg,igrid,midg -0.5297454 -1.235044 1,midg,midg; igrid,midg,midg -0.1166302 1.6295431E-02 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 2.200000 now iterating at: 13:35:52 rms-change max change #iterations 11.16785 398.0178 at 10iterations 6.689312 132.2922 at 20iterations 3.976952 75.89832 at 30iterations 2.363921 44.71372 at 40iterations 1.400151 23.01718 at 50iterations 0.8318074 14.04480 at 60iterations 0.4904196 8.016268 at 70iterations 0.2899448 5.063675 at 80iterations 0.1712321 2.882210 at 90iterations 0.1007776 1.735688 at 100iterations 5.9519116E-02 1.019674 at 110iterations 3.5055216E-02 0.6067848 at 120iterations 2.0735441E-02 0.3927860 at 130iterations 1.2324919E-02 0.2150326 at 140iterations 7.3807230E-03 0.1209221 at 150iterations 4.4725887E-03 7.3226929E-02 at 160iterations 2.7771024E-03 4.9087524E-02 at 170iterations 1.7947180E-03 3.4912109E-02 at 180iterations finished qdiffx linear iterations at : 13:36:02 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 1.7947180E-03 3.4912109E-02 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 13:36:03 11.980u 0.173s 0:12.43 97.7% 0+0k 0+0io 0pf+0w