Tue Oct 11 00:35:53 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 00:35:53 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 0.5733335 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 0.5733335 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2500 net assigned charge : 4.812020 assigned positive charge : 398.7188 centred at (gu) : 87.60725 90.16814 89.72318 assigned negative charge : -393.9075 centred at (gu) : 87.89704 90.30444 89.89264 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5700 nv = 96 ne = 84 npr = 53616 no. pairs analyzed = 53616 no. exposed pairs = 3109 no. arc points = 22200 no. surface atoms = 1054 nbur = 1597 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 222 mr = 3130 m= 0 mr = 15 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2000000 number of dielectric boundary points 2777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2205 ## 246 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7241 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5138419E-09 -1.8425658E-09 midg,1,midg; midg,igrid,midg 2.6844647E-09 -1.4996372E-09 1,midg,midg; igrid,midg,midg 9.0281942E-09 -2.2200355E-09 gauss-seidel spectral radius is 0.9842700 estimated iterations to convergence 66 setup time was (sec) 0.3800000 now iterating at: 00:35:54 rms-change max change #iterations 8.8511676E-02 14.78888 at 10iterations 7.6760612E-03 1.278839 at 20iterations 9.9712366E-04 0.2415047 at 30iterations 2.1599964E-04 5.5698395E-02 at 40iterations 5.0149662E-05 1.3175964E-02 at 50iterations finished qdiffx linear iterations at : 00:35:57 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.0149662E-05 1.3175964E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 00:35:57 3.393u 0.186s 0:03.88 92.0% 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 00:35:57 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 1.720001 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 1.720001 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2500 net assigned charge : 4.812020 assigned positive charge : 398.7188 centred at (gu) : 82.82121 90.50355 89.16897 assigned negative charge : -393.9075 centred at (gu) : 83.69106 90.91309 89.67743 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22200 grid for indexing accessible points = 1.400000 m= 19870 mr = 44244 m= 2295 mr = 14340 m= 43 mr = 1224 m= 0 mr = 5 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3335 time to turn everything in is 0.3100000 number of dielectric boundary points 25644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 19366 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) : 0.5733335 object centre at (A) : 49.14250 15.79700 13.78400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5916498E-02 -8.8980058E-05 midg,1,midg; midg,igrid,midg 1.8775888E-02 -1.8892260E-02 1,midg,midg; igrid,midg,midg 4.4489005E-03 -1.2849823E-02 gauss-seidel spectral radius is 0.9983283 estimated iterations to convergence 194 setup time was (sec) 0.5200000 now iterating at: 00:35:58 rms-change max change #iterations 3.445574 141.2119 at 10iterations 1.481244 56.04015 at 20iterations 0.6401106 22.80277 at 30iterations 0.2775259 11.35538 at 40iterations 0.1200493 4.524988 at 50iterations 5.1937908E-02 1.884898 at 60iterations 2.2689370E-02 0.8418541 at 70iterations 9.9387756E-03 0.3547754 at 80iterations 4.4000470E-03 0.1790962 at 90iterations 2.0053021E-03 7.9208374E-02 at 100iterations 9.4795664E-04 4.0195465E-02 at 110iterations 4.7555077E-04 2.0870209E-02 at 120iterations finished qdiffx linear iterations at : 00:36:05 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 4.7555077E-04 2.0870209E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 00:36:06 7.708u 0.207s 0:08.46 93.3% 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 00:36:06 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2651 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 2.580001 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): 18.09600 80.18900 ymin,ymax (A): -12.76000 44.35400 zmin,zma (A): -7.574000 35.14200 x,y,z range (A): 62.09300 57.11400 42.71600 scale (grids/A): 2.580001 object centre (A): 49.14250 15.79700 13.78400 number of atom coordinates read : 2651 total number of charged atoms : 2500 net assigned charge : 4.812020 assigned positive charge : 398.7188 centred at (gu) : 79.23177 90.75526 88.75322 assigned negative charge : -393.9075 centred at (gu) : 80.53655 91.36964 89.51627 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 147015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22200 grid for indexing accessible points = 1.400000 m= 68498 mr = 107529 m= 20301 mr = 55679 m= 3604 mr = 16009 m= 263 mr = 2558 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 11192 time to turn everything in is 0.7600000 number of dielectric boundary points 57769 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 19994 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) : 1.720001 object centre at (A) : 49.14250 15.79700 13.78400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1806206 8.2622180E-03 midg,1,midg; midg,igrid,midg 0.1833693 -0.4240564 1,midg,midg; igrid,midg,midg -6.0691215E-02 -0.1857166 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 0.9900000 now iterating at: 00:36:07 rms-change max change #iterations 8.555998 330.6933 at 10iterations 4.780107 134.2018 at 20iterations 2.665781 54.96261 at 30iterations 1.488376 31.40215 at 40iterations 0.8251483 19.18310 at 50iterations 0.4597808 9.815025 at 60iterations 0.2554304 5.399329 at 70iterations 0.1418734 2.919299 at 80iterations 7.8902505E-02 1.799232 at 90iterations 4.3962322E-02 0.9676895 at 100iterations 2.4431361E-02 0.4972076 at 110iterations 1.3657450E-02 0.3040047 at 120iterations 7.6665250E-03 0.1671143 at 130iterations 4.3419236E-03 0.1024590 at 140iterations 2.4904073E-03 6.1927795E-02 at 150iterations 1.4694314E-03 3.4801483E-02 at 160iterations 8.9750497E-04 2.3429871E-02 at 170iterations 5.7334569E-04 1.6204834E-02 at 180iterations finished qdiffx linear iterations at : 00:36:18 total time elapsed so far: 12.05000 # loops : 180 mean,max change (kT/e) : 5.7334569E-04 1.6204834E-02 energy calculations done at 12.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 00:36:19 12.182u 0.213s 0:12.92 95.8% 0+0k 0+0io 0pf+0w