Tue Oct 11 03:20:31 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 03:20:31 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 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: 0.7192791 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): 18.25000 64.63400 ymin,ymax (A): -11.82100 34.62500 zmin,zma (A): -6.9000006E-02 49.42500 x,y,z range (A): 46.38400 46.44600 49.49400 scale (grids/A): 0.7192791 object centre (A): 41.44200 11.40200 24.67800 number of atom coordinates read : 1912 total number of charged atoms : 1739 net assigned charge : 5.000006 assigned positive charge : 285.0410 centred at (gu) : 91.10577 90.28137 90.56329 assigned negative charge : -280.0412 centred at (gu) : 91.10357 90.55755 90.70966 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6691 nv = 96 ne = 84 npr = 37687 no. pairs analyzed = 37687 no. exposed pairs = 2512 no. arc points = 17933 no. surface atoms = 845 nbur = 1067 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 3561 m= 3 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1600000 number of dielectric boundary points 3528 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 113 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7136 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2543175E-07 -3.2280109E-08 midg,1,midg; midg,igrid,midg 2.0008368E-07 -1.1253203E-07 1,midg,midg; igrid,midg,midg 4.5337995E-08 7.1399640E-08 gauss-seidel spectral radius is 0.9899114 estimated iterations to convergence 81 setup time was (sec) 0.3500000 now iterating at: 03:20:32 rms-change max change #iterations 0.2030959 33.66732 at 10iterations 2.6017575E-02 3.766863 at 20iterations 3.2345320E-03 0.4426402 at 30iterations 4.1381258E-04 5.7949066E-02 at 40iterations 5.2925378E-05 9.1352463E-03 at 50iterations finished qdiffx linear iterations at : 03:20:35 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 5.2925378E-05 9.1352463E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 03:20:35 3.358u 0.186s 0:04.10 86.0% 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 03:20:35 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 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: 2.157837 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): 18.25000 64.63400 ymin,ymax (A): -11.82100 34.62500 zmin,zma (A): -6.9000006E-02 49.42500 x,y,z range (A): 46.38400 46.44600 49.49400 scale (grids/A): 2.157837 object centre (A): 41.44200 11.40200 24.67800 number of atom coordinates read : 1912 total number of charged atoms : 1739 net assigned charge : 5.000006 assigned positive charge : 285.0410 centred at (gu) : 93.31740 90.84402 91.68987 assigned negative charge : -280.0412 centred at (gu) : 93.31078 91.67296 92.12910 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70949 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17933 grid for indexing accessible points = 1.400000 m= 26545 mr = 47540 m= 4913 mr = 19515 m= 437 mr = 3097 m= 13 mr = 214 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 508 time to turn everything in is 0.3700000 number of dielectric boundary points 32489 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 13802 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) : 0.7192791 object centre at (A) : 41.44200 11.40200 24.67800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0155146E-02 -2.7044058E-02 midg,1,midg; midg,igrid,midg 7.2421990E-02 -8.6811289E-02 1,midg,midg; igrid,midg,midg 1.1043126E-02 5.5103440E-02 gauss-seidel spectral radius is 0.9988531 estimated iterations to convergence 234 setup time was (sec) 0.5700000 now iterating at: 03:20:36 rms-change max change #iterations 4.523064 227.7341 at 10iterations 2.249340 74.83441 at 20iterations 1.115351 32.75410 at 30iterations 0.5571709 18.89119 at 40iterations 0.2779702 9.378620 at 50iterations 0.1381183 4.238860 at 60iterations 6.8810701E-02 2.083029 at 70iterations 3.4306694E-02 1.010574 at 80iterations 1.7082753E-02 0.5989876 at 90iterations 8.5366946E-03 0.2962036 at 100iterations 4.2561986E-03 0.1363029 at 110iterations 2.1159083E-03 6.6074371E-02 at 120iterations finished qdiffx linear iterations at : 03:20:43 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 2.1159083E-03 6.6074371E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 03:20:44 7.804u 0.209s 0:08.55 93.5% 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 03:20:44 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 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: 3.236756 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): 18.25000 64.63400 ymin,ymax (A): -11.82100 34.62500 zmin,zma (A): -6.9000006E-02 49.42500 x,y,z range (A): 46.38400 46.44600 49.49400 scale (grids/A): 3.236756 object centre (A): 41.44200 11.40200 24.67800 number of atom coordinates read : 1912 total number of charged atoms : 1739 net assigned charge : 5.000006 assigned positive charge : 285.0410 centred at (gu) : 94.97609 91.26598 92.53490 assigned negative charge : -280.0412 centred at (gu) : 94.96639 92.50949 93.19358 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 163294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17933 grid for indexing accessible points = 1.400000 m= 83164 mr = 114947 m= 32256 mr = 67474 m= 9045 mr = 26013 m= 1714 mr = 6779 m= 188 mr = 1165 m= 4 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 1748 time to turn everything in is 1.100000 number of dielectric boundary points 73175 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 13912 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) : 2.157837 object centre at (A) : 41.44200 11.40200 24.67800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3971519 -0.4197634 midg,1,midg; midg,igrid,midg 0.4664506 -0.9897164 1,midg,midg; igrid,midg,midg 2.3829795E-02 0.5953422 gauss-seidel spectral radius is 0.9993187 estimated iterations to convergence 302 setup time was (sec) 1.330000 now iterating at: 03:20:46 rms-change max change #iterations 10.09985 332.8613 at 10iterations 6.016003 126.7850 at 20iterations 3.568003 70.06413 at 30iterations 2.107849 45.19286 at 40iterations 1.246513 25.03269 at 50iterations 0.7350197 14.32989 at 60iterations 0.4326105 7.876523 at 70iterations 0.2552157 5.368427 at 80iterations 0.1496741 3.012211 at 90iterations 8.7915398E-02 1.571716 at 100iterations 5.1701248E-02 0.8425950 at 110iterations 3.0359540E-02 0.5556259 at 120iterations 1.7828463E-02 0.3137646 at 130iterations 1.0495204E-02 0.1937408 at 140iterations 6.1644819E-03 0.1134262 at 150iterations 3.6135321E-03 6.7980289E-02 at 160iterations 2.1252960E-03 3.6712646E-02 at 170iterations 1.2480891E-03 2.1228790E-02 at 180iterations finished qdiffx linear iterations at : 03:20:57 total time elapsed so far: 12.66000 # loops : 180 mean,max change (kT/e) : 1.2480891E-03 2.1228790E-02 energy calculations done at 12.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.79000 DelPhi exited at 03:20:58 12.794u 0.199s 0:13.52 96.0% 0+0k 0+0io 0pf+0w