Sun Oct 9 13:42:52 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 13:42:52 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6932949 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): -7.102000 44.24700 ymin,ymax (A): -14.17700 36.80900 zmin,zma (A): 1.038000 44.87000 x,y,z range (A): 51.34900 50.98600 43.83200 scale (grids/A): 0.6932949 object centre (A): 18.57250 11.31600 22.95400 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.4292 centred at (gu) : 89.64371 91.23975 90.82535 assigned negative charge : -359.0236 centred at (gu) : 89.66343 91.38647 90.87216 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7763 nv = 96 ne = 84 npr = 47300 no. pairs analyzed = 47300 no. exposed pairs = 2916 no. arc points = 20397 no. surface atoms = 992 nbur = 1374 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 4346 m= 1 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1896 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4520177E-08 2.2281885E-09 midg,1,midg; midg,igrid,midg 6.3223204E-08 -5.1750600E-08 1,midg,midg; igrid,midg,midg 3.1653567E-08 1.2458170E-08 gauss-seidel spectral radius is 0.9891897 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 13:42:53 rms-change max change #iterations 0.1983978 27.46602 at 10iterations 2.4978779E-02 3.607189 at 20iterations 3.7148383E-03 0.5457611 at 30iterations 9.1829547E-04 0.1313705 at 40iterations 3.0850366E-04 4.7222137E-02 at 50iterations finished qdiffx linear iterations at : 13:42:55 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 3.0850366E-04 4.7222137E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 13:42:56 3.325u 0.170s 0:03.76 92.8% 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 13:42:56 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.079885 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): -7.102000 44.24700 ymin,ymax (A): -14.17700 36.80900 zmin,zma (A): 1.038000 44.87000 x,y,z range (A): 51.34900 50.98600 43.83200 scale (grids/A): 2.079885 object centre (A): 18.57250 11.31600 22.95400 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.4292 centred at (gu) : 88.93068 93.71880 92.47574 assigned negative charge : -359.0236 centred at (gu) : 88.99003 94.15926 92.61643 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20397 grid for indexing accessible points = 1.400000 m= 31754 mr = 57860 m= 5460 mr = 23780 m= 491 mr = 3445 m= 11 mr = 265 m= 0 mr = 1 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 101 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17645 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) : 0.6932949 object centre at (A) : 18.57250 11.31600 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1209372E-02 9.0905968E-03 midg,1,midg; midg,igrid,midg 1.3493017E-02 -4.4452004E-02 1,midg,midg; igrid,midg,midg 4.9993593E-02 -1.3030701E-02 gauss-seidel spectral radius is 0.9988241 estimated iterations to convergence 231 setup time was (sec) 0.6200000 now iterating at: 13:42:57 rms-change max change #iterations 4.889476 199.0807 at 10iterations 2.407982 80.86571 at 20iterations 1.191316 36.49164 at 30iterations 0.5915494 20.11364 at 40iterations 0.2912290 9.523573 at 50iterations 0.1451992 3.988003 at 60iterations 7.2070681E-02 2.070650 at 70iterations 3.6027197E-02 1.059410 at 80iterations 1.8112736E-02 0.5429335 at 90iterations 9.3173133E-03 0.2719498 at 100iterations 4.8916605E-03 0.1493607 at 110iterations 2.7370742E-03 9.0919495E-02 at 120iterations finished qdiffx linear iterations at : 13:43:04 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 2.7370742E-03 9.0919495E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 13:43:04 7.791u 0.185s 0:08.25 96.6% 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 13:43:04 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.119827 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): -7.102000 44.24700 ymin,ymax (A): -14.17700 36.80900 zmin,zma (A): 1.038000 44.87000 x,y,z range (A): 51.34900 50.98600 43.83200 scale (grids/A): 3.119827 object centre (A): 18.57250 11.31600 22.95400 number of atom coordinates read : 2366 total number of charged atoms : 2221 net assigned charge : 3.406020 assigned positive charge : 362.4292 centred at (gu) : 88.39596 95.57799 93.71342 assigned negative charge : -359.0236 centred at (gu) : 88.48497 96.23875 93.92452 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 190552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20397 grid for indexing accessible points = 1.400000 m= 100626 mr = 139958 m= 38456 mr = 83172 m= 10099 mr = 31113 m= 1980 mr = 7562 m= 240 mr = 1473 m= 3 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 78530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 17768 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) : 2.079885 object centre at (A) : 18.57250 11.31600 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5132350 -3.9589550E-02 midg,1,midg; midg,igrid,midg 0.2725019 -0.4833077 1,midg,midg; igrid,midg,midg 0.4495524 -0.4176894 gauss-seidel spectral radius is 0.9992970 estimated iterations to convergence 298 setup time was (sec) 1.460000 now iterating at: 13:43:06 rms-change max change #iterations 10.94222 442.7154 at 10iterations 6.489089 149.8666 at 20iterations 3.835778 70.40480 at 30iterations 2.265226 39.12991 at 40iterations 1.337986 22.75130 at 50iterations 0.7849697 13.32151 at 60iterations 0.4610447 7.512012 at 70iterations 0.2706195 5.168701 at 80iterations 0.1587512 2.585226 at 90iterations 9.3112446E-02 1.548293 at 100iterations 5.4790918E-02 1.000801 at 110iterations 3.2458257E-02 0.5450134 at 120iterations 1.9494252E-02 0.3525982 at 130iterations 1.1938518E-02 0.2255249 at 140iterations 7.6740696E-03 0.1613503 at 150iterations 5.1972927E-03 0.1112633 at 160iterations 3.7541180E-03 7.6812744E-02 at 170iterations 2.8913922E-03 6.0058594E-02 at 180iterations finished qdiffx linear iterations at : 13:43:17 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 2.8913922E-03 6.0058594E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 13:43:18 12.963u 0.217s 0:13.45 97.9% 0+0k 0+0io 0pf+0w