Mon Oct 10 13:58:46 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 13:58:46 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2806 !!! WARNING: MG8 801 has a net charge of 1.4000 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: 0.6349659 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): -45.15500 8.489000 ymin,ymax (A): -29.38400 26.68200 zmin,zma (A): -7.280000 41.68800 x,y,z range (A): 53.64400 56.06600 48.96800 scale (grids/A): 0.6349659 object centre (A): -18.33300 -1.350999 17.20400 number of atom coordinates read : 2806 total number of charged atoms : 2627 net assigned charge : -2.599971 assigned positive charge : 426.2254 centred at (gu) : 89.46646 90.80679 89.47798 assigned negative charge : -428.8261 centred at (gu) : 89.61999 90.79873 89.78465 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7712 nv = 96 ne = 84 npr = 56087 no. pairs analyzed = 56087 no. exposed pairs = 3450 no. arc points = 24304 no. surface atoms = 1165 nbur = 1641 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 450 mr = 4369 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2200000 number of dielectric boundary points 3739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2352 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9170 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3420523E-08 -3.4894484E-08 midg,1,midg; midg,igrid,midg -3.7259555E-09 -3.0766365E-09 1,midg,midg; igrid,midg,midg 1.5131331E-08 -1.8727972E-08 gauss-seidel spectral radius is 0.9871711 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 13:58:46 rms-change max change #iterations 0.1494173 21.53192 at 10iterations 1.4654246E-02 2.263021 at 20iterations 1.4583494E-03 0.1996121 at 30iterations 1.5911880E-04 2.1468639E-02 at 40iterations 3.2468564E-05 5.6591034E-03 at 50iterations finished qdiffx linear iterations at : 13:58:49 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.2468564E-05 5.6591034E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:58:50 3.418u 0.179s 0:04.29 83.4% 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 13:58:50 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2806 !!! WARNING: MG8 801 has a net charge of 1.4000 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: 1.904898 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): -45.15500 8.489000 ymin,ymax (A): -29.38400 26.68200 zmin,zma (A): -7.280000 41.68800 x,y,z range (A): 53.64400 56.06600 48.96800 scale (grids/A): 1.904898 object centre (A): -18.33300 -1.350999 17.20400 number of atom coordinates read : 2806 total number of charged atoms : 2627 net assigned charge : -2.599971 assigned positive charge : 426.2254 centred at (gu) : 88.39896 92.41998 88.43311 assigned negative charge : -428.8261 centred at (gu) : 88.85944 92.39574 89.35362 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24304 grid for indexing accessible points = 1.400000 m= 31250 mr = 59468 m= 5091 mr = 23341 m= 303 mr = 3159 m= 5 mr = 119 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1349 time to turn everything in is 0.4000000 number of dielectric boundary points 34454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20687 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) : 0.6349659 object centre at (A) : -18.33300 -1.350999 17.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3208558E-02 -8.1390992E-02 midg,1,midg; midg,igrid,midg -1.4221789E-02 -1.4168398E-02 1,midg,midg; igrid,midg,midg 5.3032026E-02 -3.3613466E-02 gauss-seidel spectral radius is 0.9986583 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 13:58:51 rms-change max change #iterations 4.502780 234.5816 at 10iterations 2.127822 67.00494 at 20iterations 1.008085 31.71687 at 30iterations 0.4763839 16.85317 at 40iterations 0.2244376 7.486924 at 50iterations 0.1060669 3.026097 at 60iterations 5.0200172E-02 1.533682 at 70iterations 2.3703910E-02 0.7978477 at 80iterations 1.1211588E-02 0.3396606 at 90iterations 5.3005256E-03 0.1501389 at 100iterations 2.5031504E-03 7.6965332E-02 at 110iterations 1.1893047E-03 3.9922714E-02 at 120iterations finished qdiffx linear iterations at : 13:58:58 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.1893047E-03 3.9922714E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 13:58:58 7.783u 0.222s 0:08.49 94.2% 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 13:58:58 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2806 !!! WARNING: MG8 801 has a net charge of 1.4000 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: 2.857347 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): -45.15500 8.489000 ymin,ymax (A): -29.38400 26.68200 zmin,zma (A): -7.280000 41.68800 x,y,z range (A): 53.64400 56.06600 48.96800 scale (grids/A): 2.857347 object centre (A): -18.33300 -1.350999 17.20400 number of atom coordinates read : 2806 total number of charged atoms : 2627 net assigned charge : -2.599971 assigned positive charge : 426.2254 centred at (gu) : 87.59821 93.62978 87.64950 assigned negative charge : -428.8261 centred at (gu) : 88.28919 93.59357 89.03026 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 194019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24304 grid for indexing accessible points = 1.400000 m= 100838 mr = 143666 m= 37070 mr = 83334 m= 9180 mr = 29948 m= 1399 mr = 6881 m= 73 mr = 966 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 4230 time to turn everything in is 1.060000 number of dielectric boundary points 77765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21013 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) : 1.904898 object centre at (A) : -18.33300 -1.350999 17.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4764202 -1.080148 midg,1,midg; midg,igrid,midg -0.2431144 -0.2899921 1,midg,midg; igrid,midg,midg 0.3933978 -0.6478146 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 1.290000 now iterating at: 13:59:00 rms-change max change #iterations 10.62983 372.7375 at 10iterations 6.277665 163.9902 at 20iterations 3.686120 70.37009 at 30iterations 2.156317 43.64635 at 40iterations 1.258921 26.41216 at 50iterations 0.7340623 13.59223 at 60iterations 0.4267294 7.635445 at 70iterations 0.2479161 4.596250 at 80iterations 0.1436470 2.707535 at 90iterations 8.3190680E-02 1.525971 at 100iterations 4.8196062E-02 0.8793221 at 110iterations 2.7949162E-02 0.4913998 at 120iterations 1.6170690E-02 0.2851725 at 130iterations 9.3473354E-03 0.1619773 at 140iterations 5.4100915E-03 9.8476410E-02 at 150iterations 3.1265828E-03 5.6755066E-02 at 160iterations 1.8158108E-03 3.2454014E-02 at 170iterations 1.0536079E-03 1.7654419E-02 at 180iterations finished qdiffx linear iterations at : 13:59:12 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 1.0536079E-03 1.7654419E-02 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 13:59:12 12.954u 0.212s 0:13.88 94.8% 0+0k 0+0io 0pf+0w