Tue Oct 11 06:28:44 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 Tue Oct 11 2011 at 06:28:44 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: HIR 46 has a net charge of 0.5140 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6955978 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): -27.34400 13.52000 ymin,ymax (A): 19.94300 64.98400 zmin,zma (A): -16.85600 34.32300 x,y,z range (A): 40.86400 45.04100 51.17900 scale (grids/A): 0.6955978 object centre (A): -6.912000 42.46350 8.733500 number of atom coordinates read : 2035 total number of charged atoms : 1922 net assigned charge : 5.945010 assigned positive charge : 313.5680 centred at (gu) : 89.16353 90.30372 90.34643 assigned negative charge : -307.6231 centred at (gu) : 89.12271 90.44988 90.39557 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6678 nv = 96 ne = 84 npr = 40396 no. pairs analyzed = 40396 no. exposed pairs = 2498 no. arc points = 17099 no. surface atoms = 854 nbur = 1181 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3779 m= 4 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1693 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7578 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2705285E-08 2.1047804E-08 midg,1,midg; midg,igrid,midg 8.6459160E-08 -1.8318477E-08 1,midg,midg; igrid,midg,midg 2.6712646E-08 4.5344187E-08 gauss-seidel spectral radius is 0.9892256 estimated iterations to convergence 78 setup time was (sec) 0.5000000 now iterating at: 06:28:45 rms-change max change #iterations 0.1892947 29.39635 at 10iterations 2.2490080E-02 3.546928 at 20iterations 2.8732731E-03 0.3861265 at 30iterations 4.4183430E-04 5.7960510E-02 at 40iterations 9.3667295E-05 1.0925293E-02 at 50iterations finished qdiffx linear iterations at : 06:28:47 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 9.3667295E-05 1.0925293E-02 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:28:48 3.336u 0.194s 0:04.01 87.7% 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 Tue Oct 11 2011 at 06:28:48 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: HIR 46 has a net charge of 0.5140 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.086793 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): -27.34400 13.52000 ymin,ymax (A): 19.94300 64.98400 zmin,zma (A): -16.85600 34.32300 x,y,z range (A): 40.86400 45.04100 51.17900 scale (grids/A): 2.086793 object centre (A): -6.912000 42.46350 8.733500 number of atom coordinates read : 2035 total number of charged atoms : 1922 net assigned charge : 5.945010 assigned positive charge : 313.5680 centred at (gu) : 87.49072 90.91102 91.03953 assigned negative charge : -307.6231 centred at (gu) : 87.36822 91.34991 91.18687 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17099 grid for indexing accessible points = 1.400000 m= 28121 mr = 50100 m= 5211 mr = 21163 m= 476 mr = 3447 m= 13 mr = 241 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 29856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15244 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) : 0.6955978 object centre at (A) : -6.912000 42.46350 8.733500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4108566E-02 4.6491753E-02 midg,1,midg; midg,igrid,midg 4.2182680E-02 2.0575437E-03 1,midg,midg; igrid,midg,midg 2.1111539E-02 1.1982989E-02 gauss-seidel spectral radius is 0.9987917 estimated iterations to convergence 228 setup time was (sec) 0.8500000 now iterating at: 06:28:49 rms-change max change #iterations 4.468390 207.2652 at 10iterations 2.193986 83.57700 at 20iterations 1.078972 34.77293 at 30iterations 0.5277734 16.60710 at 40iterations 0.2594264 8.269802 at 50iterations 0.1277183 4.503596 at 60iterations 6.2492989E-02 1.846222 at 70iterations 3.0772941E-02 0.9300351 at 80iterations 1.5257698E-02 0.5124493 at 90iterations 7.5178943E-03 0.2475529 at 100iterations 3.7382334E-03 0.1143837 at 110iterations 1.8757667E-03 6.2428951E-02 at 120iterations finished qdiffx linear iterations at : 06:28:56 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 1.8757667E-03 6.2428951E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 06:28:56 7.541u 0.239s 0:08.12 95.6% 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 Tue Oct 11 2011 at 06:28:56 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2035 !!! WARNING: HIR 46 has a net charge of 0.5140 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.130190 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): -27.34400 13.52000 ymin,ymax (A): 19.94300 64.98400 zmin,zma (A): -16.85600 34.32300 x,y,z range (A): 40.86400 45.04100 51.17900 scale (grids/A): 3.130190 object centre (A): -6.912000 42.46350 8.733500 number of atom coordinates read : 2035 total number of charged atoms : 1922 net assigned charge : 5.945010 assigned positive charge : 313.5680 centred at (gu) : 86.23613 91.36668 91.55926 assigned negative charge : -307.6231 centred at (gu) : 86.05235 92.02480 91.78033 start vw surface at 0.1300000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 163358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17099 grid for indexing accessible points = 1.400000 m= 88193 mr = 120600 m= 34950 mr = 73004 m= 9765 mr = 28486 m= 1929 mr = 7497 m= 218 mr = 1419 m= 7 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 67276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 15376 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) : 2.086793 object centre at (A) : -6.912000 42.46350 8.733500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3466325 0.4605347 midg,1,midg; midg,igrid,midg 0.3648184 5.4275962E-03 1,midg,midg; igrid,midg,midg 0.2602991 8.2695700E-02 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.920000 now iterating at: 06:28:58 rms-change max change #iterations 10.00965 426.1151 at 10iterations 5.893100 136.6006 at 20iterations 3.466558 81.80036 at 30iterations 2.030479 38.70359 at 40iterations 1.189674 22.62065 at 50iterations 0.6962182 13.72546 at 60iterations 0.4062410 8.041866 at 70iterations 0.2374507 4.890508 at 80iterations 0.1384234 2.473145 at 90iterations 8.0650829E-02 1.610119 at 100iterations 4.7278598E-02 0.8386765 at 110iterations 2.7766276E-02 0.5272255 at 120iterations 1.6364194E-02 0.2853451 at 130iterations 9.7552622E-03 0.1788101 at 140iterations 5.9374999E-03 0.1176496 at 150iterations 3.7225753E-03 8.5590363E-02 at 160iterations 2.4518471E-03 4.9007416E-02 at 170iterations 1.6983154E-03 3.4545898E-02 at 180iterations finished qdiffx linear iterations at : 06:29:09 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 1.6983154E-03 3.4545898E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 06:29:09 12.201u 0.227s 0:12.91 96.2% 0+0k 0+0io 0pf+0w