Sat Oct 8 11:36:51 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 Sat Oct 8 2011 at 11:36:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4086 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: 0.5148228 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): -3.584000 65.56600 ymin,ymax (A): -9.492000 38.82300 zmin,zma (A): -20.22500 44.84600 x,y,z range (A): 69.15000 48.31500 65.07100 scale (grids/A): 0.5148228 object centre (A): 30.99100 14.66550 12.31050 number of atom coordinates read : 4086 total number of charged atoms : 3933 net assigned charge : -7.999960 assigned positive charge : 611.9681 centred at (gu) : 88.69874 89.72958 90.56428 assigned negative charge : -619.9702 centred at (gu) : 88.74684 89.79227 90.60635 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6708 nv = 96 ne = 84 npr = 86179 no. pairs analyzed = 86179 no. exposed pairs = 4668 no. arc points = 31427 no. surface atoms = 1609 nbur = 2477 mkacc time = 0.1400000 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 = 1.652000 m= 210 mr = 3703 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2800000 number of dielectric boundary points 3212 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3185 ## 461 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 9103 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2903736E-11 -2.9182645E-10 midg,1,midg; midg,igrid,midg 3.1589724E-11 -2.8724123E-10 1,midg,midg; igrid,midg,midg -1.0770638E-11 -1.9190337E-10 gauss-seidel spectral radius is 0.9806436 estimated iterations to convergence 59 setup time was (sec) 0.5000000 now iterating at: 11:36:52 rms-change max change #iterations 6.3120089E-02 13.47583 at 10iterations 4.0925457E-03 0.7462006 at 20iterations 5.3841557E-04 7.7411652E-02 at 30iterations 1.4066037E-04 2.3143768E-02 at 40iterations 4.1049963E-05 7.0686340E-03 at 50iterations finished qdiffx linear iterations at : 11:36:55 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 4.1049963E-05 7.0686340E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:36:56 3.894u 0.236s 0:04.66 88.4% 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 11:36:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4086 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: 1.544469 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): -3.584000 65.56600 ymin,ymax (A): -9.492000 38.82300 zmin,zma (A): -20.22500 44.84600 x,y,z range (A): 69.15000 48.31500 65.07100 scale (grids/A): 1.544469 object centre (A): 30.99100 14.66550 12.31050 number of atom coordinates read : 4086 total number of charged atoms : 3933 net assigned charge : -7.999960 assigned positive charge : 611.9681 centred at (gu) : 86.09500 89.18782 91.69171 assigned negative charge : -619.9702 centred at (gu) : 86.24013 89.37617 91.81858 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 76500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31427 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22332 mr = 54527 m= 2005 mr = 15390 m= 33 mr = 889 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 736 time to turn everything in is 0.3900000 number of dielectric boundary points 30064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 417 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 29680 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) : 0.5148228 object centre at (A) : 30.99100 14.66550 12.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2358243E-03 -1.1295576E-02 midg,1,midg; midg,igrid,midg -3.7267620E-03 -9.3395924E-03 1,midg,midg; igrid,midg,midg 1.3010529E-02 -5.7247798E-03 gauss-seidel spectral radius is 0.9980585 estimated iterations to convergence 180 setup time was (sec) 0.6400000 now iterating at: 11:36:57 rms-change max change #iterations 3.535161 196.6941 at 10iterations 1.423178 53.69159 at 20iterations 0.5777560 19.23423 at 30iterations 0.2347672 8.567784 at 40iterations 9.5057771E-02 3.337704 at 50iterations 3.8671765E-02 1.428299 at 60iterations 1.5767490E-02 0.5117264 at 70iterations 6.4760135E-03 0.2322960 at 80iterations 2.6914442E-03 8.7235451E-02 at 90iterations 1.1485593E-03 3.9514542E-02 at 100iterations 5.2166812E-04 1.7997742E-02 at 110iterations 2.5965387E-04 9.5257759E-03 at 120iterations finished qdiffx linear iterations at : 11:37:04 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 2.5965387E-04 9.5257759E-03 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 11:37:05 8.588u 0.250s 0:09.28 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 Sat Oct 8 2011 at 11:37:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4086 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: 2.316703 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): -3.584000 65.56600 ymin,ymax (A): -9.492000 38.82300 zmin,zma (A): -20.22500 44.84600 x,y,z range (A): 69.15000 48.31500 65.07100 scale (grids/A): 2.316703 object centre (A): 30.99100 14.66550 12.31050 number of atom coordinates read : 4086 total number of charged atoms : 3933 net assigned charge : -7.999960 assigned positive charge : 611.9681 centred at (gu) : 84.14204 88.78120 92.53728 assigned negative charge : -619.9702 centred at (gu) : 84.35978 89.06413 92.72774 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 178642 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31427 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 80278 mr = 133565 m= 20318 mr = 63894 m= 2968 mr = 15063 m= 123 mr = 1813 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2468 time to turn everything in is 0.9300000 number of dielectric boundary points 67972 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 31384 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) : 1.544469 object centre at (A) : 30.99100 14.66550 12.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3748525 -0.2212328 midg,1,midg; midg,igrid,midg -7.6742977E-02 -0.1445098 1,midg,midg; igrid,midg,midg 0.3189430 -0.4210720 gauss-seidel spectral radius is 0.9991160 estimated iterations to convergence 266 setup time was (sec) 1.190000 now iterating at: 11:37:06 rms-change max change #iterations 9.365857 372.1846 at 10iterations 5.219428 138.9977 at 20iterations 2.898732 67.18414 at 30iterations 1.603693 30.94762 at 40iterations 0.8844614 17.82293 at 50iterations 0.4864976 9.181244 at 60iterations 0.2665273 5.354724 at 70iterations 0.1461298 2.827652 at 80iterations 8.0047563E-02 1.676186 at 90iterations 4.3862741E-02 0.8972816 at 100iterations 2.4035076E-02 0.4506588 at 110iterations 1.3171626E-02 0.2771835 at 120iterations 7.2284634E-03 0.1501732 at 130iterations 3.9828485E-03 7.8047395E-02 at 140iterations 2.2156839E-03 4.1765213E-02 at 150iterations 1.2465706E-03 2.5844574E-02 at 160iterations 7.1878114E-04 1.4395714E-02 at 170iterations 4.2929113E-04 8.9950562E-03 at 180iterations finished qdiffx linear iterations at : 11:37:19 total time elapsed so far: 13.93000 # loops : 180 mean,max change (kT/e) : 4.2929113E-04 8.9950562E-03 energy calculations done at 13.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 11:37:20 14.059u 0.278s 0:14.64 97.8% 0+0k 0+0io 0pf+0w