Mon Oct 10 17:10:18 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 Mon Oct 10 2011 at 17:10:18 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6176695 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): -26.08900 31.54700 ymin,ymax (A): -10.10200 41.00200 zmin,zma (A): 4.707000 60.20000 x,y,z range (A): 57.63600 51.10400 55.49300 scale (grids/A): 0.6176695 object centre (A): 2.729001 15.45000 32.45350 number of atom coordinates read : 2826 total number of charged atoms : 2684 net assigned charge : -1.985968 assigned positive charge : 427.1982 centred at (gu) : 91.01808 90.37306 91.39057 assigned negative charge : -429.1853 centred at (gu) : 91.12078 90.26456 91.42437 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7170 nv = 96 ne = 84 npr = 56281 no. pairs analyzed = 56281 no. exposed pairs = 3829 no. arc points = 26807 no. surface atoms = 1281 nbur = 1545 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 376 mr = 3680 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.3100000 number of dielectric boundary points 3839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2684 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8871 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5261196E-10 -5.0592628E-09 midg,1,midg; midg,igrid,midg -8.1979907E-09 6.4765309E-09 1,midg,midg; igrid,midg,midg 4.4123434E-09 -1.0688805E-08 gauss-seidel spectral radius is 0.9864526 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 17:10:19 rms-change max change #iterations 0.1294212 20.08630 at 10iterations 1.1796081E-02 1.676770 at 20iterations 1.0930140E-03 0.1462297 at 30iterations 1.0672487E-04 1.7738342E-02 at 40iterations 1.4106831E-05 2.8476715E-03 at 50iterations finished qdiffx linear iterations at : 17:10:23 total time elapsed so far: 4.070000 # loops : 50 mean,max change (kT/e) : 1.4106831E-05 2.8476715E-03 energy calculations done at 4.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 17:10:23 4.246u 0.254s 0:04.81 93.3% 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 Mon Oct 10 2011 at 17:10:23 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.853009 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): -26.08900 31.54700 ymin,ymax (A): -10.10200 41.00200 zmin,zma (A): 4.707000 60.20000 x,y,z range (A): 57.63600 51.10400 55.49300 scale (grids/A): 1.853009 object centre (A): 2.729001 15.45000 32.45350 number of atom coordinates read : 2826 total number of charged atoms : 2684 net assigned charge : -1.985968 assigned positive charge : 427.1982 centred at (gu) : 93.05335 91.11861 94.17080 assigned negative charge : -429.1853 centred at (gu) : 93.36214 90.79359 94.27278 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77553 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26807 grid for indexing accessible points = 1.400000 m= 26595 mr = 51613 m= 3875 mr = 18739 m= 183 mr = 2296 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1388 time to turn everything in is 0.5900000 number of dielectric boundary points 35505 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 21045 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) : 0.6176695 object centre at (A) : 2.729001 15.45000 32.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.2025329E-03 1.6734326E-02 midg,1,midg; midg,igrid,midg -2.9037738E-02 5.9896084E-03 1,midg,midg; igrid,midg,midg 2.6737278E-02 -5.5035695E-02 gauss-seidel spectral radius is 0.9985873 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 17:10:24 rms-change max change #iterations 4.271266 202.5694 at 10iterations 1.970412 62.78849 at 20iterations 0.9051796 30.86399 at 30iterations 0.4179730 14.32928 at 40iterations 0.1923556 7.153931 at 50iterations 8.8898048E-02 2.854518 at 60iterations 4.0793475E-02 1.366232 at 70iterations 1.8918348E-02 0.6075172 at 80iterations 8.7445816E-03 0.3093491 at 90iterations 4.0305275E-03 0.1458778 at 100iterations 1.8668482E-03 5.9661865E-02 at 110iterations 8.6170563E-04 3.1372070E-02 at 120iterations finished qdiffx linear iterations at : 17:10:33 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 8.6170563E-04 3.1372070E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 17:10:34 9.831u 0.295s 0:10.53 96.1% 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 Mon Oct 10 2011 at 17:10:34 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2826 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.779513 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): -26.08900 31.54700 ymin,ymax (A): -10.10200 41.00200 zmin,zma (A): 4.707000 60.20000 x,y,z range (A): 57.63600 51.10400 55.49300 scale (grids/A): 2.779513 object centre (A): 2.729001 15.45000 32.45350 number of atom coordinates read : 2826 total number of charged atoms : 2684 net assigned charge : -1.985968 assigned positive charge : 427.1982 centred at (gu) : 94.57977 91.67773 96.25592 assigned negative charge : -429.1853 centred at (gu) : 95.04333 91.19030 96.40898 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 179270 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26807 grid for indexing accessible points = 1.400000 m= 86347 mr = 125809 m= 30168 mr = 68607 m= 6673 mr = 23561 m= 756 mr = 4853 m= 31 mr = 503 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 4776 time to turn everything in is 1.520000 number of dielectric boundary points 79912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 21471 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) : 1.853009 object centre at (A) : 2.729001 15.45000 32.45350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6616422E-04 0.3598609 midg,1,midg; midg,igrid,midg -0.2617339 5.7559799E-02 1,midg,midg; igrid,midg,midg 0.3663784 -0.7146493 gauss-seidel spectral radius is 0.9992631 estimated iterations to convergence 291 setup time was (sec) 1.880000 now iterating at: 17:10:36 rms-change max change #iterations 10.39254 360.1750 at 10iterations 6.155949 175.7962 at 20iterations 3.619607 85.52515 at 30iterations 2.109917 42.84320 at 40iterations 1.227897 25.41904 at 50iterations 0.7118923 16.85348 at 60iterations 0.4121511 8.840729 at 70iterations 0.2383060 5.134259 at 80iterations 0.1375435 2.810289 at 90iterations 7.9193771E-02 1.527031 at 100iterations 4.5672324E-02 0.9017782 at 110iterations 2.6339270E-02 0.5465088 at 120iterations 1.5150696E-02 0.3032160 at 130iterations 8.7293992E-03 0.1615639 at 140iterations 5.0299210E-03 9.4724655E-02 at 150iterations 2.8897650E-03 5.7510376E-02 at 160iterations 1.6632365E-03 3.8125038E-02 at 170iterations 9.5957768E-04 1.7984390E-02 at 180iterations finished qdiffx linear iterations at : 17:10:50 total time elapsed so far: 15.73000 # loops : 180 mean,max change (kT/e) : 9.5957768E-04 1.7984390E-02 energy calculations done at 15.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.91000 DelPhi exited at 17:10:50 15.910u 0.317s 0:16.66 97.3% 0+0k 0+0io 0pf+0w