Sat Oct 8 11:35:34 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 Sat Oct 8 2011 at 11:35:34 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4319 !!! WARNING: HIR 439 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5454852 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): -3.305000 60.91300 ymin,ymax (A): -13.36600 38.80000 zmin,zma (A): -20.21100 45.05200 x,y,z range (A): 64.21800 52.16600 65.26300 scale (grids/A): 0.5454852 object centre (A): 28.80400 12.71700 12.42050 number of atom coordinates read : 4319 total number of charged atoms : 4175 net assigned charge : -1.485940 assigned positive charge : 653.0958 centred at (gu) : 89.10970 89.85834 90.79784 assigned negative charge : -654.5844 centred at (gu) : 89.21463 89.97001 90.89740 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8247 nv = 96 ne = 84 npr = 89527 no. pairs analyzed = 89527 no. exposed pairs = 5079 no. arc points = 34010 no. surface atoms = 1728 nbur = 2591 mkacc time = 0.1600000 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 = 1.568000 m= 338 mr = 4701 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3495 ## 436 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9632311E-10 -1.2962107E-09 midg,1,midg; midg,igrid,midg 9.9971020E-10 -1.1378749E-09 1,midg,midg; igrid,midg,midg 1.1308200E-09 -8.9070445E-10 gauss-seidel spectral radius is 0.9827668 estimated iterations to convergence 63 setup time was (sec) 0.5200000 now iterating at: 11:35:35 rms-change max change #iterations 8.9708358E-02 13.73162 at 10iterations 6.6574612E-03 0.9451590 at 20iterations 1.1166794E-03 0.1366463 at 30iterations 3.5483643E-04 4.4570923E-02 at 40iterations 1.2050287E-04 1.5434265E-02 at 50iterations finished qdiffx linear iterations at : 11:35:39 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.2050287E-04 1.5434265E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 11:35:40 3.636u 0.436s 0:05.75 70.6% 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 Sat Oct 8 2011 at 11:35:40 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4319 !!! WARNING: HIR 439 has a net charge of 0.5140 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: 1.636456 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): -3.305000 60.91300 ymin,ymax (A): -13.36600 38.80000 zmin,zma (A): -20.21100 45.05200 x,y,z range (A): 64.21800 52.16600 65.26300 scale (grids/A): 1.636456 object centre (A): 28.80400 12.71700 12.42050 number of atom coordinates read : 4319 total number of charged atoms : 4175 net assigned charge : -1.485940 assigned positive charge : 653.0958 centred at (gu) : 87.32775 89.57403 92.39246 assigned negative charge : -654.5844 centred at (gu) : 87.64341 89.90966 92.69198 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 93204 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34010 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30294 mr = 67276 m= 3250 mr = 21670 m= 84 mr = 1713 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 936 time to turn everything in is 0.4800000 number of dielectric boundary points 36171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 410 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 32014 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) : 0.5454852 object centre at (A) : 28.80400 12.71700 12.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7880941E-04 -1.2840406E-02 midg,1,midg; midg,igrid,midg 7.1507152E-03 -1.9389406E-02 1,midg,midg; igrid,midg,midg 1.9130267E-02 1.4578966E-02 gauss-seidel spectral radius is 0.9983212 estimated iterations to convergence 194 setup time was (sec) 0.7100000 now iterating at: 11:35:41 rms-change max change #iterations 4.141469 156.6500 at 10iterations 1.784897 61.41121 at 20iterations 0.7718041 23.79901 at 30iterations 0.3327539 9.945118 at 40iterations 0.1438524 4.396539 at 50iterations 6.2308975E-02 1.968405 at 60iterations 2.7113631E-02 0.8470936 at 70iterations 1.1866062E-02 0.3738861 at 80iterations 5.2083293E-03 0.1505909 at 90iterations 2.3774710E-03 7.0144653E-02 at 100iterations 1.1380080E-03 3.4580231E-02 at 110iterations 5.9394469E-04 1.8623352E-02 at 120iterations finished qdiffx linear iterations at : 11:35:49 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 5.9394469E-04 1.8623352E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 11:35:50 8.271u 0.399s 0:09.96 86.9% 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 Sat Oct 8 2011 at 11:35:50 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4319 !!! WARNING: HIR 439 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.454683 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): -3.305000 60.91300 ymin,ymax (A): -13.36600 38.80000 zmin,zma (A): -20.21100 45.05200 x,y,z range (A): 64.21800 52.16600 65.26300 scale (grids/A): 2.454683 object centre (A): 28.80400 12.71700 12.42050 number of atom coordinates read : 4319 total number of charged atoms : 4175 net assigned charge : -1.485940 assigned positive charge : 653.0958 centred at (gu) : 85.99144 89.36078 93.58841 assigned negative charge : -654.5844 centred at (gu) : 86.46486 89.86443 94.03785 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 216607 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34010 grid for indexing accessible points = 1.400000 m= 105087 mr = 163520 m= 30793 mr = 85574 m= 5163 mr = 23652 m= 301 mr = 3538 m= 5 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 3067 time to turn everything in is 1.200000 number of dielectric boundary points 81573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 38 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 33351 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) : 1.636456 object centre at (A) : 28.80400 12.71700 12.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4285818 -0.2781779 midg,1,midg; midg,igrid,midg 9.1308653E-02 -0.2703930 1,midg,midg; igrid,midg,midg 0.3816635 0.2710737 gauss-seidel spectral radius is 0.9992081 estimated iterations to convergence 281 setup time was (sec) 1.470000 now iterating at: 11:35:52 rms-change max change #iterations 10.72583 301.0314 at 10iterations 6.211992 130.0323 at 20iterations 3.563286 74.01205 at 30iterations 2.042100 38.47165 at 40iterations 1.165449 20.23465 at 50iterations 0.6629153 11.66690 at 60iterations 0.3767899 6.631685 at 70iterations 0.2135655 3.763054 at 80iterations 0.1210447 2.029423 at 90iterations 6.8555154E-02 1.263050 at 100iterations 3.8777214E-02 0.6830883 at 110iterations 2.1971371E-02 0.3967628 at 120iterations 1.2439361E-02 0.2151051 at 130iterations 7.0846053E-03 0.1244831 at 140iterations 4.0565683E-03 7.3583484E-02 at 150iterations 2.3401577E-03 3.8638115E-02 at 160iterations 1.3748514E-03 2.8319359E-02 at 170iterations 8.3401951E-04 1.5027523E-02 at 180iterations finished qdiffx linear iterations at : 11:36:10 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 8.3401951E-04 1.5027523E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.08000 DelPhi exited at 11:36:11 14.084u 1.159s 0:21.08 72.2% 0+0k 0+0io 0pf+0w