Tue Oct 11 03:47:54 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 03:47:54 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 235 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6445656 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): -12.19300 37.01100 ymin,ymax (A): -26.78500 21.73600 zmin,zma (A): -9.647000 45.58400 x,y,z range (A): 49.20400 48.52100 55.23100 scale (grids/A): 0.6445656 object centre (A): 12.40900 -2.524500 17.96850 number of atom coordinates read : 2797 total number of charged atoms : 2642 net assigned charge : 2.679016 assigned positive charge : 420.9768 centred at (gu) : 90.41594 90.34126 91.70023 assigned negative charge : -418.2983 centred at (gu) : 90.17616 90.16624 91.62531 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7883 nv = 96 ne = 84 npr = 56847 no. pairs analyzed = 56847 no. exposed pairs = 3344 no. arc points = 23513 no. surface atoms = 1125 nbur = 1672 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4518 m= 1 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.4200000 number of dielectric boundary points 3751 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2353 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9314 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5690758E-09 2.1048477E-08 midg,1,midg; midg,igrid,midg -1.9733017E-08 3.0579965E-08 1,midg,midg; igrid,midg,midg -2.8196066E-08 4.0691368E-08 gauss-seidel spectral radius is 0.9875454 estimated iterations to convergence 73 setup time was (sec) 0.7200000 now iterating at: 03:47:55 rms-change max change #iterations 0.1570306 20.22266 at 10iterations 1.6209869E-02 2.144281 at 20iterations 1.7119228E-03 0.2136841 at 30iterations 2.1990953E-04 3.0740738E-02 at 40iterations 4.7603964E-05 5.5994987E-03 at 50iterations finished qdiffx linear iterations at : 03:47:58 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 4.7603964E-05 5.5994987E-03 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.400000 DelPhi exited at 03:47:59 4.401u 0.254s 0:05.12 90.8% 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 Tue Oct 11 2011 at 03:47:59 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 235 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.933697 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): -12.19300 37.01100 ymin,ymax (A): -26.78500 21.73600 zmin,zma (A): -9.647000 45.58400 x,y,z range (A): 49.20400 48.52100 55.23100 scale (grids/A): 1.933697 object centre (A): 12.40900 -2.524500 17.96850 number of atom coordinates read : 2797 total number of charged atoms : 2642 net assigned charge : 2.679016 assigned positive charge : 420.9768 centred at (gu) : 91.24736 91.02325 95.10001 assigned negative charge : -418.2983 centred at (gu) : 90.52826 90.49854 94.87572 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 84662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23513 grid for indexing accessible points = 1.400000 m= 32620 mr = 60217 m= 5440 mr = 24695 m= 297 mr = 3471 m= 0 mr = 97 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1759 time to turn everything in is 0.7800000 number of dielectric boundary points 34539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 182 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 20821 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) : 0.6445656 object centre at (A) : 12.40900 -2.524500 17.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1955007E-02 7.8675905E-03 midg,1,midg; midg,igrid,midg -1.3804931E-02 3.0390248E-02 1,midg,midg; igrid,midg,midg -1.3296996E-02 6.2756807E-02 gauss-seidel spectral radius is 0.9986960 estimated iterations to convergence 219 setup time was (sec) 1.130000 now iterating at: 03:48:00 rms-change max change #iterations 4.553534 193.7219 at 10iterations 2.171209 70.00452 at 20iterations 1.037961 34.32503 at 30iterations 0.4959941 16.50460 at 40iterations 0.2365805 7.179492 at 50iterations 0.1132170 3.235302 at 60iterations 5.4085001E-02 1.587542 at 70iterations 2.5807183E-02 0.7813549 at 80iterations 1.2312042E-02 0.3490615 at 90iterations 5.8620409E-03 0.1737976 at 100iterations 2.8032924E-03 9.7751617E-02 at 110iterations 1.3435732E-03 4.0377617E-02 at 120iterations finished qdiffx linear iterations at : 03:48:08 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 1.3435732E-03 4.0377617E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 03:48:09 9.553u 0.219s 0:10.26 95.1% 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 03:48:09 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2797 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 235 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.900545 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): -12.19300 37.01100 ymin,ymax (A): -26.78500 21.73600 zmin,zma (A): -9.647000 45.58400 x,y,z range (A): 49.20400 48.52100 55.23100 scale (grids/A): 2.900545 object centre (A): 12.40900 -2.524500 17.96850 number of atom coordinates read : 2797 total number of charged atoms : 2642 net assigned charge : 2.679016 assigned positive charge : 420.9768 centred at (gu) : 91.87087 91.53475 97.64978 assigned negative charge : -418.2983 centred at (gu) : 90.79232 90.74772 97.31345 start vw surface at 0.2000000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 195366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23513 grid for indexing accessible points = 1.400000 m= 104114 mr = 145097 m= 39715 mr = 86723 m= 9763 mr = 32587 m= 1313 mr = 7338 m= 61 mr = 896 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 6304 time to turn everything in is 1.940000 number of dielectric boundary points 77668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 21128 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) : 1.933697 object centre at (A) : 12.40900 -2.524500 17.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4997979 0.2949531 midg,1,midg; midg,igrid,midg -0.1476171 0.3658471 1,midg,midg; igrid,midg,midg -9.9114694E-02 0.5222082 gauss-seidel spectral radius is 0.9992725 estimated iterations to convergence 293 setup time was (sec) 2.300000 now iterating at: 03:48:12 rms-change max change #iterations 10.49231 377.7908 at 10iterations 6.150187 127.4500 at 20iterations 3.591522 66.63279 at 30iterations 2.093540 36.40359 at 40iterations 1.216146 22.76281 at 50iterations 0.7077911 13.60999 at 60iterations 0.4108273 7.085281 at 70iterations 0.2379377 4.643268 at 80iterations 0.1381365 2.467485 at 90iterations 8.0117643E-02 1.309872 at 100iterations 4.6418775E-02 0.8354549 at 110iterations 2.6902771E-02 0.4486954 at 120iterations 1.5572721E-02 0.2447319 at 130iterations 9.0400418E-03 0.1542635 at 140iterations 5.2624959E-03 0.1031876 at 150iterations 3.0712918E-03 5.0460815E-02 at 160iterations 1.8126593E-03 3.5489559E-02 at 170iterations 1.0858704E-03 1.9920349E-02 at 180iterations finished qdiffx linear iterations at : 03:48:24 total time elapsed so far: 14.52000 # loops : 180 mean,max change (kT/e) : 1.0858704E-03 1.9920349E-02 energy calculations done at 14.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.75000 DelPhi exited at 03:48:25 14.752u 0.190s 0:15.39 97.0% 0+0k 0+0io 0pf+0w