Mon Oct 10 17:02:45 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 17:02:45 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 = 2815 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: 0.6199822 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): -8.526000 48.89500 ymin,ymax (A): -8.139000 39.32800 zmin,zma (A): -0.2900000 54.94200 x,y,z range (A): 57.42100 47.46700 55.23200 scale (grids/A): 0.6199822 object centre (A): 20.18450 15.59450 27.32600 number of atom coordinates read : 2815 total number of charged atoms : 2674 net assigned charge : -2.999973 assigned positive charge : 422.2622 centred at (gu) : 88.99587 89.51089 89.13732 assigned negative charge : -425.2633 centred at (gu) : 88.88546 89.40214 89.09973 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7357 nv = 96 ne = 84 npr = 55359 no. pairs analyzed = 55359 no. exposed pairs = 3782 no. arc points = 26692 no. surface atoms = 1270 nbur = 1545 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 3868 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3100000 number of dielectric boundary points 3823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2597 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0233583E-09 3.7529793E-10 midg,1,midg; midg,igrid,midg -1.1413877E-08 4.9750022E-09 1,midg,midg; igrid,midg,midg -1.2965065E-08 4.5193387E-09 gauss-seidel spectral radius is 0.9865553 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 17:02:46 rms-change max change #iterations 0.1279121 19.24328 at 10iterations 1.1607174E-02 1.822598 at 20iterations 1.0650636E-03 0.1728563 at 30iterations 9.8539655E-05 1.4509201E-02 at 40iterations 9.0513840E-06 1.3542175E-03 at 50iterations finished qdiffx linear iterations at : 17:02:49 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 9.0513840E-06 1.3542175E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 17:02:50 4.193u 0.206s 0:05.28 83.1% 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 17:02:51 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 = 2815 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: 1.859947 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): -8.526000 48.89500 ymin,ymax (A): -8.139000 39.32800 zmin,zma (A): -0.2900000 54.94200 x,y,z range (A): 57.42100 47.46700 55.23200 scale (grids/A): 1.859947 object centre (A): 20.18450 15.59450 27.32600 number of atom coordinates read : 2815 total number of charged atoms : 2674 net assigned charge : -2.999973 assigned positive charge : 422.2622 centred at (gu) : 86.98707 88.53172 87.41089 assigned negative charge : -425.2633 centred at (gu) : 86.65596 88.20609 87.29889 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 79850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26692 grid for indexing accessible points = 1.400000 m= 26809 mr = 53919 m= 3677 mr = 19009 m= 164 mr = 2052 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1417 time to turn everything in is 0.5900000 number of dielectric boundary points 35480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20951 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) : 0.6199822 object centre at (A) : 20.18450 15.59450 27.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4893883E-03 -5.0483254E-04 midg,1,midg; midg,igrid,midg -2.3581784E-02 5.8277731E-04 1,midg,midg; igrid,midg,midg -5.4927971E-02 3.0133972E-02 gauss-seidel spectral radius is 0.9986025 estimated iterations to convergence 212 setup time was (sec) 0.9100000 now iterating at: 17:02:52 rms-change max change #iterations 4.257957 159.6577 at 10iterations 1.973840 67.96595 at 20iterations 0.9128026 34.10522 at 30iterations 0.4220128 14.74174 at 40iterations 0.1957908 6.005837 at 50iterations 9.0458892E-02 2.642888 at 60iterations 4.1983098E-02 1.337095 at 70iterations 1.9439327E-02 0.6928949 at 80iterations 9.0114670E-03 0.2889063 at 90iterations 4.1798963E-03 0.1368160 at 100iterations 1.9379986E-03 6.0885429E-02 at 110iterations 9.0080895E-04 2.9776573E-02 at 120iterations finished qdiffx linear iterations at : 17:03:00 total time elapsed so far: 9.450000 # loops : 120 mean,max change (kT/e) : 9.0080895E-04 2.9776573E-02 energy calculations done at 9.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.630000 DelPhi exited at 17:03:01 9.632u 0.255s 0:10.95 90.2% 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 17:03:02 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 = 2815 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: 2.789920 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): -8.526000 48.89500 ymin,ymax (A): -8.139000 39.32800 zmin,zma (A): -0.2900000 54.94200 x,y,z range (A): 57.42100 47.46700 55.23200 scale (grids/A): 2.789920 object centre (A): 20.18450 15.59450 27.32600 number of atom coordinates read : 2815 total number of charged atoms : 2674 net assigned charge : -2.999973 assigned positive charge : 422.2622 centred at (gu) : 85.48033 87.79753 86.11615 assigned negative charge : -425.2633 centred at (gu) : 84.98386 87.30906 85.94820 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 184905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26692 grid for indexing accessible points = 1.400000 m= 88365 mr = 131366 m= 29344 mr = 70602 m= 6288 mr = 22922 m= 704 mr = 4409 m= 23 mr = 392 m= 0 mr = 6 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 4533 time to turn everything in is 1.490000 number of dielectric boundary points 79932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 21389 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) : 1.859947 object centre at (A) : 20.18450 15.59450 27.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1324537 -0.2333316 midg,1,midg; midg,igrid,midg -0.2357754 -3.5368904E-02 1,midg,midg; igrid,midg,midg -0.6275849 0.3875625 gauss-seidel spectral radius is 0.9992682 estimated iterations to convergence 292 setup time was (sec) 1.830000 now iterating at: 17:03:04 rms-change max change #iterations 10.27556 367.7423 at 10iterations 6.101975 161.7395 at 20iterations 3.584781 96.31073 at 30iterations 2.100391 49.07996 at 40iterations 1.223736 28.40459 at 50iterations 0.7114347 16.12425 at 60iterations 0.4123825 8.016665 at 70iterations 0.2391340 4.700584 at 80iterations 0.1383345 2.686788 at 90iterations 7.9852752E-02 1.538216 at 100iterations 4.6130855E-02 0.8532982 at 110iterations 2.6603721E-02 0.4705353 at 120iterations 1.5356199E-02 0.2710190 at 130iterations 8.8769346E-03 0.1725807 at 140iterations 5.1116305E-03 9.6741676E-02 at 150iterations 2.9511198E-03 5.4953814E-02 at 160iterations 1.7007207E-03 3.3343226E-02 at 170iterations 9.8001130E-04 1.6427994E-02 at 180iterations finished qdiffx linear iterations at : 17:03:17 total time elapsed so far: 15.39000 # loops : 180 mean,max change (kT/e) : 9.8001130E-04 1.6427994E-02 energy calculations done at 15.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.57000 DelPhi exited at 17:03:18 15.576u 0.276s 0:16.39 96.6% 0+0k 0+0io 0pf+0w