Sat Oct 15 15:35:12 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 Sat Oct 15 2011 at 15:35:12 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6901365 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): -40.84700 0.2750000 ymin,ymax (A): -27.20700 18.68200 zmin,zma (A): -17.27000 34.31400 x,y,z range (A): 41.12200 45.88900 51.58400 scale (grids/A): 0.6901365 object centre (A): -20.28600 -4.262501 8.521999 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.9760 centred at (gu) : 90.80482 89.86710 89.86501 assigned negative charge : -314.0311 centred at (gu) : 90.84405 89.99752 89.82438 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6732 nv = 96 ne = 84 npr = 42044 no. pairs analyzed = 42044 no. exposed pairs = 2560 no. arc points = 17370 no. surface atoms = 862 nbur = 1227 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3852 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 7.9999991E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1675 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7623 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9910768E-08 4.5430330E-08 midg,1,midg; midg,igrid,midg 7.8244298E-08 -1.0833555E-08 1,midg,midg; igrid,midg,midg 3.9477388E-08 2.3098023E-08 gauss-seidel spectral radius is 0.9890603 estimated iterations to convergence 78 setup time was (sec) 0.4100000 now iterating at: 15:35:13 rms-change max change #iterations 0.1792940 25.87639 at 10iterations 2.1656053E-02 2.961376 at 20iterations 2.7450875E-03 0.4351807 at 30iterations 4.4424724E-04 5.4841995E-02 at 40iterations 1.0199079E-04 1.3534546E-02 at 50iterations finished qdiffx linear iterations at : 15:35:16 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 1.0199079E-04 1.3534546E-02 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 15:35:17 3.967u 0.256s 0:04.92 85.5% 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 Sat Oct 15 2011 at 15:35:17 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.070410 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): -40.84700 0.2750000 ymin,ymax (A): -27.20700 18.68200 zmin,zma (A): -17.27000 34.31400 x,y,z range (A): 41.12200 45.88900 51.58400 scale (grids/A): 2.070410 object centre (A): -20.28600 -4.262501 8.521999 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.9760 centred at (gu) : 92.41460 89.60115 89.59509 assigned negative charge : -314.0311 centred at (gu) : 92.53223 89.99255 89.47306 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17370 grid for indexing accessible points = 1.400000 m= 27775 mr = 50695 m= 5168 mr = 20956 m= 404 mr = 3374 m= 2 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 29614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15495 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) : 0.6901365 object centre at (A) : -20.28600 -4.262501 8.521999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7176937E-02 3.3800229E-02 midg,1,midg; midg,igrid,midg 3.6189187E-02 3.4947421E-03 1,midg,midg; igrid,midg,midg 1.7975938E-02 2.0712268E-02 gauss-seidel spectral radius is 0.9987800 estimated iterations to convergence 227 setup time was (sec) 0.6700000 now iterating at: 15:35:18 rms-change max change #iterations 4.425092 180.9985 at 10iterations 2.160925 74.24971 at 20iterations 1.054792 33.14078 at 30iterations 0.5182025 17.57297 at 40iterations 0.2517509 9.011421 at 50iterations 0.1238740 4.024010 at 60iterations 6.0484026E-02 1.965887 at 70iterations 2.9672043E-02 0.8891528 at 80iterations 1.4587092E-02 0.4140854 at 90iterations 7.1967598E-03 0.2415285 at 100iterations 3.5656395E-03 0.1069069 at 110iterations 1.7971033E-03 6.9375277E-02 at 120iterations finished qdiffx linear iterations at : 15:35:30 total time elapsed so far: 8.980000 # loops : 120 mean,max change (kT/e) : 1.7971033E-03 6.9375277E-02 energy calculations done at 8.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.110000 DelPhi exited at 15:35:31 9.118u 0.304s 0:14.54 64.7% 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 Sat Oct 15 2011 at 15:35:31 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.105614 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): -40.84700 0.2750000 ymin,ymax (A): -27.20700 18.68200 zmin,zma (A): -17.27000 34.31400 x,y,z range (A): 41.12200 45.88900 51.58400 scale (grids/A): 3.105614 object centre (A): -20.28600 -4.262501 8.521999 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.9760 centred at (gu) : 93.62192 89.40163 89.39248 assigned negative charge : -314.0311 centred at (gu) : 93.79852 89.98891 89.20959 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 164922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17370 grid for indexing accessible points = 1.400000 m= 87449 mr = 121896 m= 34390 mr = 72652 m= 9684 mr = 28238 m= 1810 mr = 7406 m= 157 mr = 1349 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 66801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 15636 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) : 2.070410 object centre at (A) : -20.28600 -4.262501 8.521999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3010970 0.2314624 midg,1,midg; midg,igrid,midg 0.3155879 3.8239092E-02 1,midg,midg; igrid,midg,midg 0.1425133 0.2013774 gauss-seidel spectral radius is 0.9992814 estimated iterations to convergence 294 setup time was (sec) 1.420000 now iterating at: 15:35:34 rms-change max change #iterations 10.01882 387.5901 at 10iterations 5.875568 130.6772 at 20iterations 3.440957 68.85597 at 30iterations 2.012449 39.64988 at 40iterations 1.176423 21.96967 at 50iterations 0.6867758 12.81200 at 60iterations 0.4001527 7.880102 at 70iterations 0.2329489 4.409647 at 80iterations 0.1359317 2.550358 at 90iterations 7.9212666E-02 1.496651 at 100iterations 4.6348035E-02 0.9255276 at 110iterations 2.7142983E-02 0.5577126 at 120iterations 1.6037835E-02 0.3027973 at 130iterations 9.6359346E-03 0.1904907 at 140iterations 5.9136911E-03 0.1174545 at 150iterations 3.7679335E-03 7.3722839E-02 at 160iterations 2.5320165E-03 4.7271729E-02 at 170iterations 1.7891405E-03 3.1000137E-02 at 180iterations finished qdiffx linear iterations at : 15:35:53 total time elapsed so far: 14.49000 # loops : 180 mean,max change (kT/e) : 1.7891405E-03 3.1000137E-02 energy calculations done at 14.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.62000 DelPhi exited at 15:35:53 14.618u 0.307s 0:21.78 68.4% 0+0k 0+0io 0pf+0w