Tue Oct 11 06:08:11 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 06:08:11 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: SEP 172 has a net charge of -0.4750 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: 0.7011324 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): 6.583000 50.89300 ymin,ymax (A): 16.99100 57.79300 zmin,zma (A): -2.599000 48.17600 x,y,z range (A): 44.31000 40.80200 50.77500 scale (grids/A): 0.7011324 object centre (A): 28.73800 37.39200 22.78850 number of atom coordinates read : 2053 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 312.1171 centred at (gu) : 90.34222 89.74893 89.86670 assigned negative charge : -305.0922 centred at (gu) : 90.15920 89.77443 89.88740 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6811 nv = 96 ne = 84 npr = 41468 no. pairs analyzed = 41468 no. exposed pairs = 2489 no. arc points = 17039 no. surface atoms = 853 nbur = 1200 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 3899 m= 7 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1586 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0948807E-08 4.1004345E-08 midg,1,midg; midg,igrid,midg 6.4448834E-08 3.8190400E-08 1,midg,midg; igrid,midg,midg -2.5484498E-08 1.3496084E-07 gauss-seidel spectral radius is 0.9893940 estimated iterations to convergence 79 setup time was (sec) 0.3400000 now iterating at: 06:08:12 rms-change max change #iterations 0.1923451 29.44186 at 10iterations 2.4100030E-02 3.609243 at 20iterations 3.1305412E-03 0.3980865 at 30iterations 5.2567053E-04 7.1365356E-02 at 40iterations 1.3164767E-04 1.5155792E-02 at 50iterations finished qdiffx linear iterations at : 06:08:15 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.3164767E-04 1.5155792E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 06:08:15 3.356u 0.183s 0:04.17 84.6% 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 06:08:15 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: SEP 172 has a net charge of -0.4750 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: 2.103397 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): 6.583000 50.89300 ymin,ymax (A): 16.99100 57.79300 zmin,zma (A): -2.599000 48.17600 x,y,z range (A): 44.31000 40.80200 50.77500 scale (grids/A): 2.103397 object centre (A): 28.73800 37.39200 22.78850 number of atom coordinates read : 2053 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 312.1171 centred at (gu) : 91.02660 89.24657 89.60012 assigned negative charge : -305.0922 centred at (gu) : 90.47776 89.32323 89.66236 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 28295 mr = 51114 m= 5349 mr = 21171 m= 476 mr = 3451 m= 13 mr = 212 m= 0 mr = 3 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 30436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15304 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) : 0.7011324 object centre at (A) : 28.73800 37.39200 22.78850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7952339E-02 5.3389549E-02 midg,1,midg; midg,igrid,midg 2.8660197E-02 3.6588197E-03 1,midg,midg; igrid,midg,midg 1.0961479E-02 4.4389345E-02 gauss-seidel spectral radius is 0.9988105 estimated iterations to convergence 230 setup time was (sec) 0.5700000 now iterating at: 06:08:16 rms-change max change #iterations 4.470932 180.2747 at 10iterations 2.194438 71.00160 at 20iterations 1.078537 33.54376 at 30iterations 0.5355982 15.98248 at 40iterations 0.2640113 8.877275 at 50iterations 0.1302164 3.911289 at 60iterations 6.4464614E-02 1.912607 at 70iterations 3.1847827E-02 0.9154091 at 80iterations 1.5842356E-02 0.4934769 at 90iterations 7.9095149E-03 0.2550869 at 100iterations 3.9743111E-03 0.1346283 at 110iterations 2.0423334E-03 6.6310883E-02 at 120iterations finished qdiffx linear iterations at : 06:08:23 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 2.0423334E-03 6.6310883E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 06:08:24 7.796u 0.210s 0:08.51 94.0% 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 06:08:24 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2053 !!! WARNING: SEP 172 has a net charge of -0.4750 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: 3.155096 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): 6.583000 50.89300 ymin,ymax (A): 16.99100 57.79300 zmin,zma (A): -2.599000 48.17600 x,y,z range (A): 44.31000 40.80200 50.77500 scale (grids/A): 3.155096 object centre (A): 28.73800 37.39200 22.78850 number of atom coordinates read : 2053 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 312.1171 centred at (gu) : 91.53992 88.86988 89.40016 assigned negative charge : -305.0922 centred at (gu) : 90.71667 88.98489 89.49356 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 166591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 89078 mr = 123198 m= 35144 mr = 73717 m= 9938 mr = 28430 m= 1876 mr = 7507 m= 199 mr = 1294 m= 5 mr = 112 m= 0 mr = 2 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.110000 number of dielectric boundary points 68571 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 15412 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) : 2.103397 object centre at (A) : 28.73800 37.39200 22.78850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4102274 0.4846479 midg,1,midg; midg,igrid,midg 0.2185518 2.1629308E-03 1,midg,midg; igrid,midg,midg 0.1901171 0.3404393 gauss-seidel spectral radius is 0.9992893 estimated iterations to convergence 296 setup time was (sec) 1.350000 now iterating at: 06:08:26 rms-change max change #iterations 10.01194 318.7853 at 10iterations 5.905530 137.1852 at 20iterations 3.484098 72.88337 at 30iterations 2.048723 42.84240 at 40iterations 1.204509 24.96772 at 50iterations 0.7056247 13.78689 at 60iterations 0.4138531 7.631029 at 70iterations 0.2421542 4.632692 at 80iterations 0.1414500 2.878553 at 90iterations 8.2940787E-02 1.583824 at 100iterations 4.8590172E-02 0.8250656 at 110iterations 2.8578861E-02 0.5216980 at 120iterations 1.6967228E-02 0.3097763 at 130iterations 1.0201718E-02 0.1896515 at 140iterations 6.2926412E-03 0.1186981 at 150iterations 4.0022698E-03 8.4812164E-02 at 160iterations 2.6928780E-03 5.4061890E-02 at 170iterations 1.9058585E-03 3.8612366E-02 at 180iterations finished qdiffx linear iterations at : 06:08:37 total time elapsed so far: 12.61000 # loops : 180 mean,max change (kT/e) : 1.9058585E-03 3.8612366E-02 energy calculations done at 12.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.74000 DelPhi exited at 06:08:38 12.747u 0.208s 0:13.62 95.0% 0+0k 0+0io 0pf+0w