Mon Oct 10 09:17:21 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+sph.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 = amb.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 09:17:21 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1027 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7449413 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): -32.12800 3.761000 ymin,ymax (A): 14.82500 55.90800 zmin,zma (A): -3.690000 44.09900 x,y,z range (A): 35.88900 41.08300 47.78900 scale (grids/A): 0.7449413 object centre (A): -14.18350 35.36650 20.20450 number of atom coordinates read : 1027 total number of charged atoms : 901 net assigned charge : 2.500001 assigned positive charge : 142.5031 centred at (gu) : 90.20176 91.26086 88.22415 assigned negative charge : -140.0030 centred at (gu) : 90.17846 91.05721 88.41887 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4085 nv = 96 ne = 84 npr = 20269 no. pairs analyzed = 20269 no. exposed pairs = 1538 no. arc points = 11390 no. surface atoms = 517 nbur = 510 mkacc time = 3.0000005E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 300 mr = 1905 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 4.0000003E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1000000 number of dielectric boundary points 2434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 859 ## 70 charges are in solution ## iepsmp to db, and charging done at 0.1600000 number of grid points assigned charge 3937 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9467494E-07 -3.6027142E-08 midg,1,midg; midg,igrid,midg -4.3493461E-08 1.8187448E-07 1,midg,midg; igrid,midg,midg 3.3064861E-08 5.9179200E-08 gauss-seidel spectral radius is 0.9905064 estimated iterations to convergence 83 setup time was (sec) 0.2900000 now iterating at: 09:17:22 rms-change max change #iterations 0.1601420 32.58241 at 10iterations 2.1445954E-02 4.336492 at 20iterations 2.8608993E-03 0.5742188 at 30iterations 3.8206828E-04 6.8668365E-02 at 40iterations 5.0641422E-05 9.1819763E-03 at 50iterations finished qdiffx linear iterations at : 09:17:25 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.0641422E-05 9.1819763E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 09:17:25 3.319u 0.186s 0:03.77 92.5% 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 Mon Oct 10 2011 at 09:17:25 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1027 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.234824 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): -32.12800 3.761000 ymin,ymax (A): 14.82500 55.90800 zmin,zma (A): -3.690000 44.09900 x,y,z range (A): 35.88900 41.08300 47.78900 scale (grids/A): 2.234824 object centre (A): -14.18350 35.36650 20.20450 number of atom coordinates read : 1027 total number of charged atoms : 901 net assigned charge : 2.500001 assigned positive charge : 142.5031 centred at (gu) : 90.60557 93.78271 84.67252 assigned negative charge : -140.0030 centred at (gu) : 90.53528 93.17163 85.25652 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 41657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11390 grid for indexing accessible points = 1.400000 m= 15555 mr = 25187 m= 3368 mr = 11093 m= 377 mr = 2202 m= 9 mr = 169 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 22315 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 7181 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) : 0.7449413 object centre at (A) : -14.18350 35.36650 20.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8743433E-02 6.5081287E-03 midg,1,midg; midg,igrid,midg -1.4049511E-02 1.6694361E-02 1,midg,midg; igrid,midg,midg 1.7551498E-03 1.5598753E-02 gauss-seidel spectral radius is 0.9988447 estimated iterations to convergence 233 setup time was (sec) 0.4600000 now iterating at: 09:17:26 rms-change max change #iterations 3.321535 219.2557 at 10iterations 1.634857 75.86369 at 20iterations 0.8082894 34.32006 at 30iterations 0.4008019 17.31233 at 40iterations 0.1983695 8.593231 at 50iterations 9.8142602E-02 3.814600 at 60iterations 4.8344441E-02 1.865582 at 70iterations 2.4094287E-02 0.9358292 at 80iterations 1.1915918E-02 0.4809456 at 90iterations 5.9065288E-03 0.2439137 at 100iterations 2.9150140E-03 0.1162353 at 110iterations 1.4517064E-03 5.4775000E-02 at 120iterations finished qdiffx linear iterations at : 09:17:33 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.4517064E-03 5.4775000E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 09:17:33 7.647u 0.187s 0:08.20 95.3% 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 Mon Oct 10 2011 at 09:17:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1027 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 3.352236 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): -32.12800 3.761000 ymin,ymax (A): 14.82500 55.90800 zmin,zma (A): -3.690000 44.09900 x,y,z range (A): 35.88900 41.08300 47.78900 scale (grids/A): 3.352236 object centre (A): -14.18350 35.36650 20.20450 number of atom coordinates read : 1027 total number of charged atoms : 901 net assigned charge : 2.500001 assigned positive charge : 142.5031 centred at (gu) : 90.90836 95.67416 82.00888 assigned negative charge : -140.0030 centred at (gu) : 90.80289 94.75739 82.88478 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 95591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11390 grid for indexing accessible points = 1.400000 m= 46888 mr = 61185 m= 19973 mr = 36960 m= 6519 mr = 16125 m= 1453 mr = 4889 m= 167 mr = 974 m= 6 mr = 86 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 50376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 7208 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) : 2.234824 object centre at (A) : -14.18350 35.36650 20.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1884079 4.8682097E-02 midg,1,midg; midg,igrid,midg -8.4160589E-02 2.6499577E-02 1,midg,midg; igrid,midg,midg -2.3448253E-02 0.1233711 gauss-seidel spectral radius is 0.9993062 estimated iterations to convergence 300 setup time was (sec) 0.8800000 now iterating at: 09:17:34 rms-change max change #iterations 7.375620 265.6591 at 10iterations 4.348372 119.9104 at 20iterations 2.550536 62.03808 at 30iterations 1.497637 41.27492 at 40iterations 0.8734440 23.20915 at 50iterations 0.5105656 12.37622 at 60iterations 0.2993115 7.000381 at 70iterations 0.1738250 4.081261 at 80iterations 0.1017637 2.241058 at 90iterations 5.9141245E-02 1.362253 at 100iterations 3.4496833E-02 0.8770159 at 110iterations 2.0088216E-02 0.5441648 at 120iterations 1.1749890E-02 0.2562084 at 130iterations 6.8336269E-03 0.1430454 at 140iterations 3.9980379E-03 9.1339111E-02 at 150iterations 2.3278426E-03 5.0880432E-02 at 160iterations 1.3528663E-03 3.0464172E-02 at 170iterations 7.8998925E-04 1.7549515E-02 at 180iterations finished qdiffx linear iterations at : 09:17:45 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 7.8998925E-04 1.7549515E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 09:17:46 11.696u 0.213s 0:12.44 95.6% 0+0k 0+0io 0pf+0w