Mon Oct 10 14:01:01 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 14:01:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1670 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: 0.7615625 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): -38.49700 8.249001 ymin,ymax (A): 2.552000 49.18800 zmin,zma (A): 31.42400 73.43800 x,y,z range (A): 46.74600 46.63600 42.01400 scale (grids/A): 0.7615625 object centre (A): -15.12400 25.87000 52.43100 number of atom coordinates read : 1670 total number of charged atoms : 1532 net assigned charge : 5.500009 assigned positive charge : 244.9854 centred at (gu) : 90.00394 90.02735 89.95776 assigned negative charge : -239.4853 centred at (gu) : 90.01945 89.92165 90.04503 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6923 nv = 96 ne = 84 npr = 31944 no. pairs analyzed = 31944 no. exposed pairs = 2384 no. arc points = 16874 no. surface atoms = 797 nbur = 873 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 582 mr = 3642 m= 7 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 43 time to turn everything in is 0.2500000 number of dielectric boundary points 3769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1139 ## 79 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5567849E-07 4.9864145E-08 midg,1,midg; midg,igrid,midg 2.8200118E-08 2.7621255E-07 1,midg,midg; igrid,midg,midg 1.7073604E-07 1.3477141E-07 gauss-seidel spectral radius is 0.9909765 estimated iterations to convergence 85 setup time was (sec) 0.4700000 now iterating at: 14:01:02 rms-change max change #iterations 0.2387576 35.61708 at 10iterations 3.3472862E-02 4.932442 at 20iterations 4.8342547E-03 0.6579514 at 30iterations 6.8747776E-04 9.8768711E-02 at 40iterations 1.0747864E-04 1.4270782E-02 at 50iterations finished qdiffx linear iterations at : 14:01:05 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.0747864E-04 1.4270782E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:01:05 3.327u 0.162s 0:03.92 88.7% 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 14:01:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1670 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: 2.284688 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): -38.49700 8.249001 ymin,ymax (A): 2.552000 49.18800 zmin,zma (A): 31.42400 73.43800 x,y,z range (A): 46.74600 46.63600 42.01400 scale (grids/A): 2.284688 object centre (A): -15.12400 25.87000 52.43100 number of atom coordinates read : 1670 total number of charged atoms : 1532 net assigned charge : 5.500009 assigned positive charge : 244.9854 centred at (gu) : 90.01199 90.08228 89.87362 assigned negative charge : -239.4853 centred at (gu) : 90.05870 89.76508 90.13512 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 29380 mr = 48022 m= 7507 mr = 21707 m= 976 mr = 5248 m= 42 mr = 535 m= 0 mr = 10 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1042 time to turn everything in is 0.6200000 number of dielectric boundary points 34519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 12219 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) : 0.7615625 object centre at (A) : -15.12400 25.87000 52.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8621662E-02 -2.8210662E-02 midg,1,midg; midg,igrid,midg 2.1026565E-02 0.1201409 1,midg,midg; igrid,midg,midg 2.5762361E-02 -1.1492352E-02 gauss-seidel spectral radius is 0.9989541 estimated iterations to convergence 245 setup time was (sec) 0.9500000 now iterating at: 14:01:06 rms-change max change #iterations 4.604817 187.9342 at 10iterations 2.368328 80.46432 at 20iterations 1.212574 39.34842 at 30iterations 0.6255869 19.32789 at 40iterations 0.3213258 9.617563 at 50iterations 0.1651563 5.453525 at 60iterations 8.5231982E-02 2.544771 at 70iterations 4.3895319E-02 1.291723 at 80iterations 2.2636324E-02 0.7348629 at 90iterations 1.1649335E-02 0.3587430 at 100iterations 6.0170796E-03 0.1856194 at 110iterations 3.0983638E-03 0.1005402 at 120iterations finished qdiffx linear iterations at : 14:01:13 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 3.0983638E-03 0.1005402 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:01:14 7.808u 0.211s 0:08.92 89.7% 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 14:01:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1670 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: 3.427031 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): -38.49700 8.249001 ymin,ymax (A): 2.552000 49.18800 zmin,zma (A): 31.42400 73.43800 x,y,z range (A): 46.74600 46.63600 42.01400 scale (grids/A): 3.427031 object centre (A): -15.12400 25.87000 52.43100 number of atom coordinates read : 1670 total number of charged atoms : 1532 net assigned charge : 5.500009 assigned positive charge : 244.9854 centred at (gu) : 90.01795 90.12349 89.81050 assigned negative charge : -239.4853 centred at (gu) : 90.08808 89.64766 90.20266 start vw surface at 0.1800000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 166160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16874 grid for indexing accessible points = 1.400000 m= 87489 mr = 116397 m= 40048 mr = 70916 m= 14670 mr = 32681 m= 3747 mr = 11666 m= 580 mr = 2819 m= 33 mr = 386 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 3436 time to turn everything in is 1.930000 number of dielectric boundary points 77852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 12256 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) : 2.284688 object centre at (A) : -15.12400 25.87000 52.43100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1677844 -0.3360102 midg,1,midg; midg,igrid,midg 0.1441898 1.459382 1,midg,midg; igrid,midg,midg 0.4582081 -0.5126696 gauss-seidel spectral radius is 0.9993317 estimated iterations to convergence 305 setup time was (sec) 2.280000 now iterating at: 14:01:17 rms-change max change #iterations 10.02577 309.8340 at 10iterations 6.064797 148.4135 at 20iterations 3.657736 84.22261 at 30iterations 2.192964 39.03683 at 40iterations 1.312142 24.49839 at 50iterations 0.7833538 15.03152 at 60iterations 0.4674028 8.189569 at 70iterations 0.2779460 5.040226 at 80iterations 0.1654410 2.888283 at 90iterations 9.8278418E-02 1.703317 at 100iterations 5.8483090E-02 1.054207 at 110iterations 3.4708258E-02 0.5971756 at 120iterations 2.0541832E-02 0.3577642 at 130iterations 1.2198720E-02 0.2303629 at 140iterations 7.2526047E-03 0.1512498 at 150iterations 4.3083630E-03 8.1707001E-02 at 160iterations 2.5745018E-03 4.5284271E-02 at 170iterations 1.5516588E-03 2.7753353E-02 at 180iterations finished qdiffx linear iterations at : 14:01:28 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 1.5516588E-03 2.7753353E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 14:01:29 13.418u 0.274s 0:14.89 91.8% 0+0k 0+0io 0pf+0w