Mon Oct 10 19:32:23 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+sph.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 = amb.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 19:32:23 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2727 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: 0.6089322 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): -12.72100 45.74200 ymin,ymax (A): -27.99100 24.96400 zmin,zma (A): -12.88400 45.18700 x,y,z range (A): 58.46300 52.95500 58.07100 scale (grids/A): 0.6089322 object centre (A): 16.51050 -1.513500 16.15150 number of atom coordinates read : 2727 total number of charged atoms : 2588 net assigned charge : -2.999985 assigned positive charge : 404.9166 centred at (gu) : 89.78407 90.70158 90.42789 assigned negative charge : -407.9178 centred at (gu) : 89.81502 90.71918 90.46834 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6926 nv = 96 ne = 84 npr = 54410 no. pairs analyzed = 54410 no. exposed pairs = 3772 no. arc points = 26735 no. surface atoms = 1251 nbur = 1476 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 3419 m= 4 mr = 34 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 0.2000000 number of dielectric boundary points 3841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2647 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8376 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9110414E-10 -4.1209391E-09 midg,1,midg; midg,igrid,midg -7.0564565E-10 -3.0214284E-09 1,midg,midg; igrid,midg,midg -1.4795673E-10 -3.1100493E-09 gauss-seidel spectral radius is 0.9860608 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 19:32:23 rms-change max change #iterations 0.1180572 17.46285 at 10iterations 1.0451320E-02 1.633814 at 20iterations 1.0563964E-03 0.1616812 at 30iterations 1.6919040E-04 3.0418396E-02 at 40iterations 4.1303967E-05 8.1863403E-03 at 50iterations finished qdiffx linear iterations at : 19:32:26 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 4.1303967E-05 8.1863403E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 19:32:27 3.429u 0.187s 0:04.41 81.6% 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 Mon Oct 10 2011 at 19:32:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2727 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: 1.826797 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): -12.72100 45.74200 ymin,ymax (A): -27.99100 24.96400 zmin,zma (A): -12.88400 45.18700 x,y,z range (A): 58.46300 52.95500 58.07100 scale (grids/A): 1.826797 object centre (A): 16.51050 -1.513500 16.15150 number of atom coordinates read : 2727 total number of charged atoms : 2588 net assigned charge : -2.999985 assigned positive charge : 404.9166 centred at (gu) : 89.35171 92.10426 91.28305 assigned negative charge : -407.9178 centred at (gu) : 89.44502 92.15739 91.40498 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74035 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26735 grid for indexing accessible points = 1.400000 m= 25677 mr = 48847 m= 3928 mr = 17644 m= 221 mr = 2081 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 35252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20200 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) : 0.6089322 object centre at (A) : 16.51050 -1.513500 16.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4216995E-03 -4.4523571E-02 midg,1,midg; midg,igrid,midg 7.5182337E-03 -5.1663495E-03 1,midg,midg; igrid,midg,midg 1.7782988E-02 -6.7160735E-03 gauss-seidel spectral radius is 0.9985510 estimated iterations to convergence 208 setup time was (sec) 0.5900000 now iterating at: 19:32:28 rms-change max change #iterations 4.059617 168.0537 at 10iterations 1.841459 75.95313 at 20iterations 0.8409937 26.67094 at 30iterations 0.3842751 12.69443 at 40iterations 0.1753676 6.382442 at 50iterations 8.0271460E-02 2.759728 at 60iterations 3.6707789E-02 1.292616 at 70iterations 1.6850673E-02 0.5997752 at 80iterations 7.7386061E-03 0.2447510 at 90iterations 3.5713401E-03 0.1274800 at 100iterations 1.6541319E-03 5.6794763E-02 at 110iterations 7.7887235E-04 2.8751373E-02 at 120iterations finished qdiffx linear iterations at : 19:32:36 total time elapsed so far: 8.610000 # loops : 120 mean,max change (kT/e) : 7.7887235E-04 2.8751373E-02 energy calculations done at 8.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.750000 DelPhi exited at 19:32:37 8.755u 0.196s 0:10.05 88.9% 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 Mon Oct 10 2011 at 19:32:37 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2727 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: 2.740195 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): -12.72100 45.74200 ymin,ymax (A): -27.99100 24.96400 zmin,zma (A): -12.88400 45.18700 x,y,z range (A): 58.46300 52.95500 58.07100 scale (grids/A): 2.740195 object centre (A): 16.51050 -1.513500 16.15150 number of atom coordinates read : 2727 total number of charged atoms : 2588 net assigned charge : -2.999985 assigned positive charge : 404.9166 centred at (gu) : 89.02746 93.15613 91.92454 assigned negative charge : -407.9178 centred at (gu) : 89.16757 93.23591 92.10744 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26735 grid for indexing accessible points = 1.400000 m= 82720 mr = 119434 m= 29582 mr = 64730 m= 6759 mr = 22361 m= 775 mr = 4511 m= 42 mr = 381 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9500000 number of dielectric boundary points 79646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 20690 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) : 1.826797 object centre at (A) : 16.51050 -1.513500 16.15150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1037938 -0.5329859 midg,1,midg; midg,igrid,midg 0.1807942 4.6106324E-02 1,midg,midg; igrid,midg,midg 0.2023997 -0.1076108 gauss-seidel spectral radius is 0.9992476 estimated iterations to convergence 288 setup time was (sec) 1.170000 now iterating at: 19:32:39 rms-change max change #iterations 9.841179 360.7523 at 10iterations 5.805982 149.6350 at 20iterations 3.385817 96.59647 at 30iterations 1.965314 44.96670 at 40iterations 1.137490 21.90146 at 50iterations 0.6566709 15.42636 at 60iterations 0.3788038 8.093924 at 70iterations 0.2175322 4.221058 at 80iterations 0.1251959 2.454750 at 90iterations 7.1742140E-02 1.330604 at 100iterations 4.1136906E-02 0.7963285 at 110iterations 2.3544427E-02 0.4601135 at 120iterations 1.3483386E-02 0.2642593 at 130iterations 7.7221035E-03 0.1514691 at 140iterations 4.4431728E-03 8.9802742E-02 at 150iterations 2.5452038E-03 4.9055099E-02 at 160iterations 1.4641004E-03 2.6494980E-02 at 170iterations 8.4743201E-04 1.6449809E-02 at 180iterations finished qdiffx linear iterations at : 19:32:50 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 8.4743201E-04 1.6449809E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 19:32:51 12.735u 0.227s 0:13.91 93.0% 0+0k 0+0io 0pf+0w