Tue Oct 11 05:16:40 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 05:16:40 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 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: 0.6894682 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): 16.83600 63.01900 ymin,ymax (A): -3.558000 33.57200 zmin,zma (A): 20.45200 72.08600 x,y,z range (A): 46.18300 37.13000 51.63400 scale (grids/A): 0.6894682 object centre (A): 39.92750 15.00700 46.26900 number of atom coordinates read : 2272 total number of charged atoms : 1947 net assigned charge : 5.931010 assigned positive charge : 315.5640 centred at (gu) : 90.98325 89.69939 89.23913 assigned negative charge : -309.6331 centred at (gu) : 91.12225 89.72295 89.18958 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6764 nv = 96 ne = 84 npr = 41579 no. pairs analyzed = 41579 no. exposed pairs = 2594 no. arc points = 17347 no. surface atoms = 880 nbur = 1392 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3873 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1676 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9306206E-08 4.2209265E-08 midg,1,midg; midg,igrid,midg 4.3062631E-08 2.3912087E-08 1,midg,midg; igrid,midg,midg 6.3764183E-08 -1.6149297E-08 gauss-seidel spectral radius is 0.9890391 estimated iterations to convergence 78 setup time was (sec) 0.4700000 now iterating at: 05:16:41 rms-change max change #iterations 0.1803192 25.37579 at 10iterations 2.1209471E-02 3.028748 at 20iterations 2.9386801E-03 0.4248734 at 30iterations 5.5517489E-04 6.3659668E-02 at 40iterations 1.5364474E-04 1.8024921E-02 at 50iterations finished qdiffx linear iterations at : 05:16:43 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 1.5364474E-04 1.8024921E-02 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 05:16:44 3.240u 0.177s 0:03.77 90.4% 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 05:16:44 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.068405 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): 16.83600 63.01900 ymin,ymax (A): -3.558000 33.57200 zmin,zma (A): 20.45200 72.08600 x,y,z range (A): 46.18300 37.13000 51.63400 scale (grids/A): 2.068405 object centre (A): 39.92750 15.00700 46.26900 number of atom coordinates read : 2272 total number of charged atoms : 1947 net assigned charge : 5.931010 assigned positive charge : 315.5640 centred at (gu) : 92.94968 89.09808 87.71745 assigned negative charge : -309.6331 centred at (gu) : 93.36690 89.16883 87.56878 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 71748 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 28604 mr = 51043 m= 5307 mr = 21719 m= 415 mr = 3459 m= 7 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 29642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15435 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) : 0.6894682 object centre at (A) : 39.92750 15.00700 46.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7047824E-02 3.6497563E-02 midg,1,midg; midg,igrid,midg 2.0484356E-02 1.0044504E-02 1,midg,midg; igrid,midg,midg 2.5976175E-02 1.0868787E-02 gauss-seidel spectral radius is 0.9987760 estimated iterations to convergence 226 setup time was (sec) 0.7900000 now iterating at: 05:16:45 rms-change max change #iterations 4.362524 181.5372 at 10iterations 2.138647 75.12407 at 20iterations 1.040439 37.87690 at 30iterations 0.5122731 17.29120 at 40iterations 0.2507256 8.104483 at 50iterations 0.1223119 4.113531 at 60iterations 6.0166866E-02 1.967024 at 70iterations 2.9571900E-02 0.9824581 at 80iterations 1.4668419E-02 0.4554443 at 90iterations 7.3351120E-03 0.2330399 at 100iterations 3.7172681E-03 0.1159039 at 110iterations 1.9742304E-03 6.4949036E-02 at 120iterations finished qdiffx linear iterations at : 05:16:51 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 1.9742304E-03 6.4949036E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.110000 DelPhi exited at 05:16:52 7.110u 0.170s 0:07.86 92.6% 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 Tue Oct 11 2011 at 05:16:52 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2272 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: GLM 174 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: 3.102607 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): 16.83600 63.01900 ymin,ymax (A): -3.558000 33.57200 zmin,zma (A): 20.45200 72.08600 x,y,z range (A): 46.18300 37.13000 51.63400 scale (grids/A): 3.102607 object centre (A): 39.92750 15.00700 46.26900 number of atom coordinates read : 2272 total number of charged atoms : 1947 net assigned charge : 5.931010 assigned positive charge : 315.5640 centred at (gu) : 94.42437 88.64729 86.57608 assigned negative charge : -309.6331 centred at (gu) : 95.05041 88.75324 86.35314 start vw surface at 0.1500000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 165138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17347 grid for indexing accessible points = 1.400000 m= 89768 mr = 122743 m= 35835 mr = 74682 m= 10049 mr = 29472 m= 1838 mr = 7810 m= 201 mr = 1326 m= 3 mr = 127 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 66670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.790000 number of grid points assigned charge 15576 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) : 2.068405 object centre at (A) : 39.92750 15.00700 46.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4220392 0.2629664 midg,1,midg; midg,igrid,midg 0.1850028 7.8693934E-02 1,midg,midg; igrid,midg,midg 0.2304818 0.3433628 gauss-seidel spectral radius is 0.9992818 estimated iterations to convergence 294 setup time was (sec) 1.970000 now iterating at: 05:16:54 rms-change max change #iterations 9.840721 395.8965 at 10iterations 5.803929 123.0153 at 20iterations 3.411452 66.54282 at 30iterations 2.001162 54.47497 at 40iterations 1.172841 23.71370 at 50iterations 0.6836171 13.46785 at 60iterations 0.3998703 7.325820 at 70iterations 0.2333139 4.317543 at 80iterations 0.1361520 2.783679 at 90iterations 7.9330206E-02 1.408295 at 100iterations 4.6218365E-02 0.8102760 at 110iterations 2.7107475E-02 0.4975128 at 120iterations 1.5936187E-02 0.3052959 at 130iterations 9.4925910E-03 0.1794434 at 140iterations 5.7569798E-03 0.1170120 at 150iterations 3.5879267E-03 6.6436768E-02 at 160iterations 2.3629179E-03 4.1927338E-02 at 170iterations 1.6492222E-03 3.2638550E-02 at 180iterations finished qdiffx linear iterations at : 05:17:04 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 1.6492222E-03 3.2638550E-02 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 05:17:05 12.334u 0.177s 0:12.99 96.2% 0+0k 0+0io 0pf+0w