Sun Oct 9 07:37:21 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 Sun Oct 9 2011 at 07:37:21 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 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: 0.7216997 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): 5.867000 49.00700 ymin,ymax (A): 20.48000 69.80800 zmin,zma (A): -6.330000 34.73000 x,y,z range (A): 43.14000 49.32800 41.06000 scale (grids/A): 0.7216997 object centre (A): 27.43700 45.14400 14.20000 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 254.0242 centred at (gu) : 90.10654 89.55943 89.37238 assigned negative charge : -264.1241 centred at (gu) : 90.19340 89.47576 89.67255 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5921 nv = 96 ne = 84 npr = 36851 no. pairs analyzed = 36851 no. exposed pairs = 2123 no. arc points = 14618 no. surface atoms = 718 nbur = 980 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3329 m= 1 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2300000 number of dielectric boundary points 2885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1221 ## 90 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6425 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.4780607E-08 -2.6253184E-07 midg,1,midg; midg,igrid,midg -1.8187887E-07 -6.6334167E-08 1,midg,midg; igrid,midg,midg -6.8600372E-08 -1.7266859E-07 gauss-seidel spectral radius is 0.9899543 estimated iterations to convergence 81 setup time was (sec) 0.4400000 now iterating at: 07:37:22 rms-change max change #iterations 0.2017058 30.83343 at 10iterations 2.5949353E-02 3.915611 at 20iterations 3.2843885E-03 0.4692841 at 30iterations 4.1946539E-04 5.7652473E-02 at 40iterations 5.4021330E-05 8.5482597E-03 at 50iterations finished qdiffx linear iterations at : 07:37:24 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 5.4021330E-05 8.5482597E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 07:37:25 3.065u 0.151s 0:03.48 92.2% 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 Sun Oct 9 2011 at 07:37:25 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 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: 2.165099 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): 5.867000 49.00700 ymin,ymax (A): 20.48000 69.80800 zmin,zma (A): -6.330000 34.73000 x,y,z range (A): 43.14000 49.32800 41.06000 scale (grids/A): 2.165099 object centre (A): 27.43700 45.14400 14.20000 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 254.0242 centred at (gu) : 90.31973 88.67843 88.11728 assigned negative charge : -264.1241 centred at (gu) : 90.58021 88.42735 89.01793 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14618 grid for indexing accessible points = 1.400000 m= 25003 mr = 43343 m= 5017 mr = 19346 m= 448 mr = 3595 m= 8 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1529 time to turn everything in is 0.5300000 number of dielectric boundary points 26538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12436 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) : 0.7216997 object centre at (A) : 27.43700 45.14400 14.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2090316E-02 -6.9155507E-02 midg,1,midg; midg,igrid,midg -7.0500590E-02 -9.2605380E-03 1,midg,midg; igrid,midg,midg -3.1018633E-02 -5.9723403E-02 gauss-seidel spectral radius is 0.9988339 estimated iterations to convergence 232 setup time was (sec) 0.7800000 now iterating at: 07:37:26 rms-change max change #iterations 4.429620 241.7889 at 10iterations 2.189174 100.8630 at 20iterations 1.085480 35.31097 at 30iterations 0.5370150 16.26657 at 40iterations 0.2658377 8.229249 at 50iterations 0.1321658 4.272327 at 60iterations 6.5569930E-02 2.048162 at 70iterations 3.2527581E-02 0.9983177 at 80iterations 1.6109483E-02 0.4923015 at 90iterations 7.9857158E-03 0.2656336 at 100iterations 3.9533065E-03 0.1253014 at 110iterations 1.9635705E-03 6.9798470E-02 at 120iterations finished qdiffx linear iterations at : 07:37:32 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 1.9635705E-03 6.9798470E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 07:37:32 6.976u 0.179s 0:07.44 95.9% 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 Sun Oct 9 2011 at 07:37:32 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1698 !!! WARNING: MN1 160 has a net charge of 1.4000 !!! WARNING: NAP 161 has a net charge of -2.0000 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: 3.247648 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): 5.867000 49.00700 ymin,ymax (A): 20.48000 69.80800 zmin,zma (A): -6.330000 34.73000 x,y,z range (A): 43.14000 49.32800 41.06000 scale (grids/A): 3.247648 object centre (A): 27.43700 45.14400 14.20000 number of atom coordinates read : 1698 total number of charged atoms : 1561 net assigned charge : -10.09999 assigned positive charge : 254.0242 centred at (gu) : 90.47958 88.01752 87.17605 assigned negative charge : -264.1241 centred at (gu) : 90.87035 87.64101 88.52686 start vw surface at 0.1400000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 144001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14618 grid for indexing accessible points = 1.400000 m= 76557 mr = 103900 m= 32587 mr = 64047 m= 9717 mr = 27574 m= 1938 mr = 7958 m= 227 mr = 1541 m= 9 mr = 149 m= 0 mr = 5 time to grow re-entrant surface = 0.6700001 no. cavity mid-points inaccessible to solvent = 5088 time to turn everything in is 1.470000 number of dielectric boundary points 59862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 12488 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) : 2.165099 object centre at (A) : 27.43700 45.14400 14.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2751860 -0.4858961 midg,1,midg; midg,igrid,midg -0.5861377 -2.0151308E-02 1,midg,midg; igrid,midg,midg -0.1814694 -0.4178698 gauss-seidel spectral radius is 0.9992874 estimated iterations to convergence 296 setup time was (sec) 1.750000 now iterating at: 07:37:34 rms-change max change #iterations 9.731915 540.3083 at 10iterations 5.605646 138.2632 at 20iterations 3.246773 75.64214 at 30iterations 1.882258 41.03545 at 40iterations 1.092592 22.11779 at 50iterations 0.6317172 11.14117 at 60iterations 0.3661733 7.579113 at 70iterations 0.2119026 4.122743 at 80iterations 0.1228557 2.183305 at 90iterations 7.1111917E-02 1.300621 at 100iterations 4.1209619E-02 0.7121511 at 110iterations 2.3863208E-02 0.4397922 at 120iterations 1.3822797E-02 0.2542610 at 130iterations 8.0432398E-03 0.1545334 at 140iterations 4.6536736E-03 9.3614578E-02 at 150iterations 2.6955113E-03 5.1792145E-02 at 160iterations 1.5681915E-03 3.2630920E-02 at 170iterations 9.0607628E-04 1.5932083E-02 at 180iterations finished qdiffx linear iterations at : 07:37:44 total time elapsed so far: 11.32000 # loops : 180 mean,max change (kT/e) : 9.0607628E-04 1.5932083E-02 energy calculations done at 11.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 07:37:44 11.499u 0.188s 0:11.95 97.6% 0+0k 0+0io 0pf+0w