Mon Oct 10 01:21:49 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 Mon Oct 10 2011 at 01:21:49 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 0.6289641 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): -5.737000 34.92700 ymin,ymax (A): -3.560000 48.46600 zmin,zma (A): -24.47300 32.12800 x,y,z range (A): 40.66400 52.02600 56.60100 scale (grids/A): 0.6289641 object centre (A): 14.59500 22.45300 3.827501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.5999 centred at (gu) : 90.76297 92.53117 89.95242 assigned negative charge : -289.6003 centred at (gu) : 90.85712 92.66441 89.89744 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5414 nv = 96 ne = 84 npr = 39772 no. pairs analyzed = 39772 no. exposed pairs = 2490 no. arc points = 17430 no. surface atoms = 850 nbur = 1120 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 299 mr = 3027 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2636 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1771 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.2686850E-11 6.8448465E-09 midg,1,midg; midg,igrid,midg 6.8379205E-09 -9.2783718E-09 1,midg,midg; igrid,midg,midg 7.9374765E-09 -3.1165810E-09 gauss-seidel spectral radius is 0.9868534 estimated iterations to convergence 71 setup time was (sec) 0.5200000 now iterating at: 01:21:50 rms-change max change #iterations 0.1172614 21.55836 at 10iterations 1.1039437E-02 2.009701 at 20iterations 1.0567731E-03 0.1606274 at 30iterations 9.8615455E-05 1.6998291E-02 at 40iterations 9.4434663E-06 1.5068054E-03 at 50iterations finished qdiffx linear iterations at : 01:21:53 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 9.4434663E-06 1.5068054E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 01:21:53 3.597u 0.224s 0:04.11 92.7% 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 01:21:53 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 1.886892 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): -5.737000 34.92700 ymin,ymax (A): -3.560000 48.46600 zmin,zma (A): -24.47300 32.12800 x,y,z range (A): 40.66400 52.02600 56.60100 scale (grids/A): 1.886892 object centre (A): 14.59500 22.45300 3.827501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.5999 centred at (gu) : 92.28891 97.59352 89.85706 assigned negative charge : -289.6003 centred at (gu) : 92.57159 97.99349 89.69238 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 22050 mr = 39790 m= 3484 mr = 16964 m= 173 mr = 2313 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2441 time to turn everything in is 0.5100000 number of dielectric boundary points 24376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 14420 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) : 0.6289641 object centre at (A) : 14.59500 22.45300 3.827501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6417981E-02 1.9620134E-02 midg,1,midg; midg,igrid,midg 2.6201218E-02 -9.0628676E-03 1,midg,midg; igrid,midg,midg 6.7844726E-03 -4.5184810E-03 gauss-seidel spectral radius is 0.9985338 estimated iterations to convergence 207 setup time was (sec) 0.8400000 now iterating at: 01:21:54 rms-change max change #iterations 3.561470 163.7890 at 10iterations 1.615232 73.83859 at 20iterations 0.7377505 30.29427 at 30iterations 0.3368346 11.62715 at 40iterations 0.1528748 5.346800 at 50iterations 6.9906734E-02 2.790428 at 60iterations 3.1813648E-02 1.199476 at 70iterations 1.4462637E-02 0.5312922 at 80iterations 6.5862872E-03 0.2249126 at 90iterations 3.0166041E-03 0.1349564 at 100iterations 1.3645256E-03 4.8774719E-02 at 110iterations 6.2315317E-04 2.4320602E-02 at 120iterations finished qdiffx linear iterations at : 01:22:01 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 6.2315317E-04 2.4320602E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 01:22:02 8.149u 0.215s 0:08.65 96.5% 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 Mon Oct 10 2011 at 01:22:02 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: 248 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 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: 2.830339 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): -5.737000 34.92700 ymin,ymax (A): -3.560000 48.46600 zmin,zma (A): -24.47300 32.12800 x,y,z range (A): 40.66400 52.02600 56.60100 scale (grids/A): 2.830339 object centre (A): 14.59500 22.45300 3.827501 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.5999 centred at (gu) : 93.43326 101.3903 89.78555 assigned negative charge : -289.6003 centred at (gu) : 93.85746 101.9903 89.53866 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 133267 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 69999 mr = 95996 m= 26888 mr = 58450 m= 6298 mr = 22515 m= 807 mr = 4889 m= 33 mr = 564 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 7814 time to turn everything in is 1.100000 number of dielectric boundary points 54862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 14702 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) : 1.886892 object centre at (A) : 14.59500 22.45300 3.827501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.070233 8.8745788E-02 midg,1,midg; midg,igrid,midg 0.2773254 -0.1220754 1,midg,midg; igrid,midg,midg 4.6214432E-02 -3.3221703E-02 gauss-seidel spectral radius is 0.9992162 estimated iterations to convergence 282 setup time was (sec) 1.400000 now iterating at: 01:22:04 rms-change max change #iterations 8.483260 387.6232 at 10iterations 4.856994 134.8331 at 20iterations 2.764874 70.04289 at 30iterations 1.571384 36.68482 at 40iterations 0.8894881 18.65243 at 50iterations 0.5043593 11.84386 at 60iterations 0.2850891 5.877459 at 70iterations 0.1612390 3.303984 at 80iterations 9.1003679E-02 1.944668 at 90iterations 5.1562257E-02 1.027122 at 100iterations 2.9085927E-02 0.6598811 at 110iterations 1.6398774E-02 0.3388839 at 120iterations 9.2773167E-03 0.1837816 at 130iterations 5.2334899E-03 0.1060219 at 140iterations 2.9525058E-03 5.7928085E-02 at 150iterations 1.6674098E-03 3.5084724E-02 at 160iterations 9.3973579E-04 1.8554688E-02 at 170iterations 5.3101266E-04 1.0139465E-02 at 180iterations finished qdiffx linear iterations at : 01:22:14 total time elapsed so far: 11.75000 # loops : 180 mean,max change (kT/e) : 5.3101266E-04 1.0139465E-02 energy calculations done at 11.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.94000 DelPhi exited at 01:22:14 11.944u 0.205s 0:12.43 97.6% 0+0k 0+0io 0pf+0w