Sun Oct 9 00:22:17 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 Sun Oct 9 2011 at 00:22:17 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 = 2261 !!! WARNING: ARG 36 has a net charge of -0.2720 !!! WARNING: VAL 44 has a net charge of 0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6682434 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): -27.18900 26.08500 ymin,ymax (A): 7.893000 50.87700 zmin,zma (A): -12.81400 39.30200 x,y,z range (A): 53.27400 42.98400 52.11600 scale (grids/A): 0.6682434 object centre (A): -0.5520000 29.38500 13.24400 number of atom coordinates read : 2261 total number of charged atoms : 2126 net assigned charge : 10.75403 assigned positive charge : 330.2685 centred at (gu) : 90.46425 90.67805 91.53104 assigned negative charge : -319.5151 centred at (gu) : 90.42999 90.64252 91.48624 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6931 nv = 96 ne = 84 npr = 45583 no. pairs analyzed = 45583 no. exposed pairs = 2959 no. arc points = 21111 no. surface atoms = 990 nbur = 1271 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 452 mr = 3654 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1800000 number of dielectric boundary points 3669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1996 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8427988E-08 5.8165874E-08 midg,1,midg; midg,igrid,midg 2.3318993E-08 4.6780741E-08 1,midg,midg; igrid,midg,midg 2.4535384E-08 4.4531813E-08 gauss-seidel spectral radius is 0.9883683 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 00:22:18 rms-change max change #iterations 0.1564848 23.08807 at 10iterations 1.7171767E-02 2.798123 at 20iterations 1.9334549E-03 0.2662697 at 30iterations 2.7358186E-04 4.9057007E-02 at 40iterations 6.9140835E-05 1.3450623E-02 at 50iterations finished qdiffx linear iterations at : 00:22:21 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 6.9140835E-05 1.3450623E-02 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 00:22:22 3.684u 0.209s 0:04.18 92.8% 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 Sun Oct 9 2011 at 00:22:22 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 = 2261 !!! WARNING: ARG 36 has a net charge of -0.2720 !!! WARNING: VAL 44 has a net charge of 0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.004730 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): -27.18900 26.08500 ymin,ymax (A): 7.893000 50.87700 zmin,zma (A): -12.81400 39.30200 x,y,z range (A): 53.27400 42.98400 52.11600 scale (grids/A): 2.004730 object centre (A): -0.5520000 29.38500 13.24400 number of atom coordinates read : 2261 total number of charged atoms : 2126 net assigned charge : 10.75403 assigned positive charge : 330.2685 centred at (gu) : 91.39237 92.03389 94.59283 assigned negative charge : -319.5151 centred at (gu) : 91.29014 91.92766 94.45894 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21111 grid for indexing accessible points = 1.400000 m= 27693 mr = 49920 m= 5041 mr = 19957 m= 411 mr = 3217 m= 3 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1173 time to turn everything in is 0.3800000 number of dielectric boundary points 33720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16811 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) : 0.6682434 object centre at (A) : -0.5520000 29.38500 13.24400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3062957E-02 3.0104330E-02 midg,1,midg; midg,igrid,midg 1.1832351E-02 2.9294169E-02 1,midg,midg; igrid,midg,midg 4.9185310E-02 6.2369887E-02 gauss-seidel spectral radius is 0.9987383 estimated iterations to convergence 223 setup time was (sec) 0.6200000 now iterating at: 00:22:23 rms-change max change #iterations 4.172427 224.4383 at 10iterations 2.016364 66.29622 at 20iterations 0.9662620 31.61136 at 30iterations 0.4647511 14.18904 at 40iterations 0.2237030 7.561417 at 50iterations 0.1077648 3.404934 at 60iterations 5.2097380E-02 1.509634 at 70iterations 2.5099961E-02 0.7305546 at 80iterations 1.2090503E-02 0.3801079 at 90iterations 5.8552306E-03 0.1879015 at 100iterations 2.8504215E-03 9.5769882E-02 at 110iterations 1.4018591E-03 5.0836563E-02 at 120iterations finished qdiffx linear iterations at : 00:22:30 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.4018591E-03 5.0836563E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.370000 DelPhi exited at 00:22:31 8.377u 0.226s 0:08.89 96.6% 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 Sun Oct 9 2011 at 00:22:31 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 = 2261 !!! WARNING: ARG 36 has a net charge of -0.2720 !!! WARNING: VAL 44 has a net charge of 0.0260 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.007095 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): -27.18900 26.08500 ymin,ymax (A): 7.893000 50.87700 zmin,zma (A): -12.81400 39.30200 x,y,z range (A): 53.27400 42.98400 52.11600 scale (grids/A): 3.007095 object centre (A): -0.5520000 29.38500 13.24400 number of atom coordinates read : 2261 total number of charged atoms : 2126 net assigned charge : 10.75403 assigned positive charge : 330.2685 centred at (gu) : 92.08855 93.05093 96.88910 assigned negative charge : -319.5151 centred at (gu) : 91.93517 92.89168 96.68853 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21111 grid for indexing accessible points = 1.400000 m= 86992 mr = 120887 m= 33929 mr = 70313 m= 9380 mr = 26940 m= 1702 mr = 7081 m= 150 mr = 1169 m= 3 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 4019 time to turn everything in is 0.9900000 number of dielectric boundary points 75978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 17008 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) : 2.004730 object centre at (A) : -0.5520000 29.38500 13.24400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4667211 0.3480182 midg,1,midg; midg,igrid,midg 5.6784332E-02 0.2534725 1,midg,midg; igrid,midg,midg 0.4615534 0.5501994 gauss-seidel spectral radius is 0.9992911 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 00:22:32 rms-change max change #iterations 9.810797 422.4960 at 10iterations 5.847899 150.2962 at 20iterations 3.448411 78.30807 at 30iterations 2.032174 42.43881 at 40iterations 1.196092 24.42239 at 50iterations 0.7030057 16.41842 at 60iterations 0.4106559 7.603549 at 70iterations 0.2405420 4.362175 at 80iterations 0.1405888 2.938435 at 90iterations 8.2279682E-02 1.475060 at 100iterations 4.7871217E-02 0.9683571 at 110iterations 2.7916893E-02 0.5072021 at 120iterations 1.6316339E-02 0.2928543 at 130iterations 9.5112855E-03 0.1727123 at 140iterations 5.5410522E-03 0.1046419 at 150iterations 3.2371324E-03 5.5778503E-02 at 160iterations 1.8934489E-03 3.6786079E-02 at 170iterations 1.1170468E-03 2.1127701E-02 at 180iterations finished qdiffx linear iterations at : 00:22:45 total time elapsed so far: 13.88000 # loops : 180 mean,max change (kT/e) : 1.1170468E-03 2.1127701E-02 energy calculations done at 13.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.02000 DelPhi exited at 00:22:45 14.018u 0.258s 0:14.60 97.6% 0+0k 0+0io 0pf+0w