Mon Oct 10 09:17:46 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 Mon Oct 10 2011 at 09:17:46 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: 251 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: 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 : 144.9030 centred at (gu) : 90.05947 91.27884 88.27622 assigned negative charge : -142.4030 centred at (gu) : 90.02808 91.08123 88.47724 start vw surface at 5.0000001E-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 1.9920647E-07 -3.9973933E-08 midg,1,midg; midg,igrid,midg -4.2274518E-08 1.8094578E-07 1,midg,midg; igrid,midg,midg 2.9683232E-08 6.1915848E-08 gauss-seidel spectral radius is 0.9905064 estimated iterations to convergence 83 setup time was (sec) 0.2800000 now iterating at: 09:17:47 rms-change max change #iterations 0.1671908 32.58232 at 10iterations 2.2561278E-02 4.268437 at 20iterations 3.0064641E-03 0.5681992 at 30iterations 4.0152142E-04 7.5248718E-02 at 40iterations 5.3035379E-05 9.4470978E-03 at 50iterations finished qdiffx linear iterations at : 09:17:49 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 5.3035379E-05 9.4470978E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 09:17:51 3.216u 0.179s 0:04.99 67.7% 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 Mon Oct 10 2011 at 09:17:51 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: 251 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 : 144.9030 centred at (gu) : 90.17863 93.83662 84.82867 assigned negative charge : -142.4030 centred at (gu) : 90.08418 93.24376 85.43169 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1100000 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 = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 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 0.3000000 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 3.8484443E-02 7.9945717E-03 midg,1,midg; midg,igrid,midg -1.4069649E-02 1.6759399E-02 1,midg,midg; igrid,midg,midg 2.0089457E-03 1.5675914E-02 gauss-seidel spectral radius is 0.9988447 estimated iterations to convergence 233 setup time was (sec) 0.4300000 now iterating at: 09:17:52 rms-change max change #iterations 3.392529 219.2557 at 10iterations 1.671134 75.86370 at 20iterations 0.8263652 34.30219 at 30iterations 0.4093567 17.09467 at 40iterations 0.2026755 8.907772 at 50iterations 0.1004003 4.057230 at 60iterations 4.9426202E-02 1.842146 at 70iterations 2.4617909E-02 0.9802780 at 80iterations 1.2183951E-02 0.4844112 at 90iterations 6.0368320E-03 0.2351151 at 100iterations 2.9832083E-03 0.1183375 at 110iterations 1.4847064E-03 5.8089972E-02 at 120iterations finished qdiffx linear iterations at : 09:17:59 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 1.4847064E-03 5.8089972E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 09:17:59 7.407u 0.189s 0:07.99 94.8% 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 09:17:59 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: 251 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 : 144.9030 centred at (gu) : 90.26791 95.75503 82.24310 assigned negative charge : -142.4030 centred at (gu) : 90.12627 94.86562 83.14755 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3000000 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 0.6800000 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 0.7500000 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 0.1845399 6.4202689E-02 midg,1,midg; midg,igrid,midg -8.4215589E-02 2.6986251E-02 1,midg,midg; igrid,midg,midg -1.0346101E-02 0.1237680 gauss-seidel spectral radius is 0.9993062 estimated iterations to convergence 300 setup time was (sec) 0.9000000 now iterating at: 09:18:00 rms-change max change #iterations 7.528645 300.6275 at 10iterations 4.435822 119.9130 at 20iterations 2.600826 62.02917 at 30iterations 1.527031 41.27517 at 40iterations 0.8904292 23.37023 at 50iterations 0.5200402 12.57618 at 60iterations 0.3049773 6.969292 at 70iterations 0.1770824 4.099797 at 80iterations 0.1037033 2.305679 at 90iterations 6.0246516E-02 1.355938 at 100iterations 3.5149191E-02 0.8857457 at 110iterations 2.0451894E-02 0.5330979 at 120iterations 1.1969943E-02 0.2623158 at 130iterations 6.9582206E-03 0.1428251 at 140iterations 4.0722373E-03 9.4314575E-02 at 150iterations 2.3716337E-03 5.2211761E-02 at 160iterations 1.3784762E-03 3.0578613E-02 at 170iterations 8.0478151E-04 1.8108368E-02 at 180iterations finished qdiffx linear iterations at : 09:18:11 total time elapsed so far: 11.59000 # loops : 180 mean,max change (kT/e) : 8.0478151E-04 1.8108368E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 09:18:12 11.726u 0.192s 0:12.32 96.6% 0+0k 0+0io 0pf+0w