Mon Oct 10 14:09:56 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 Mon Oct 10 2011 at 14:09:56 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2181 !!! WARNING: LYS 209 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6487826 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): -22.03300 24.21200 ymin,ymax (A): -53.41900 -8.839001 zmin,zma (A): -34.72500 20.14700 x,y,z range (A): 46.24500 44.58000 54.87200 scale (grids/A): 0.6487826 object centre (A): 1.089500 -31.12900 -7.288999 number of atom coordinates read : 2181 total number of charged atoms : 2040 net assigned charge : -7.271978 assigned positive charge : 327.6438 centred at (gu) : 89.34274 90.62638 91.57253 assigned negative charge : -334.9159 centred at (gu) : 89.37507 90.68845 91.69189 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6170 nv = 96 ne = 84 npr = 44278 no. pairs analyzed = 44278 no. exposed pairs = 2868 no. arc points = 20458 no. surface atoms = 965 nbur = 1216 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 331 mr = 3224 m= 0 mr = 24 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3253 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1911 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7266 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0650157E-09 -3.9905636E-08 midg,1,midg; midg,igrid,midg -4.8066360E-09 -2.4120514E-08 1,midg,midg; igrid,midg,midg -1.0413471E-08 -1.5154214E-08 gauss-seidel spectral radius is 0.9876558 estimated iterations to convergence 74 setup time was (sec) 0.6300000 now iterating at: 14:09:57 rms-change max change #iterations 0.1430672 24.41471 at 10iterations 1.4657196E-02 2.156031 at 20iterations 1.4734040E-03 0.2561278 at 30iterations 1.5152036E-04 2.3090363E-02 at 40iterations 1.5240718E-05 2.2659302E-03 at 50iterations finished qdiffx linear iterations at : 14:10:01 total time elapsed so far: 5.150000 # loops : 50 mean,max change (kT/e) : 1.5240718E-05 2.2659302E-03 energy calculations done at 5.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.330000 DelPhi exited at 14:10:02 5.333u 0.442s 0:06.51 88.6% 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 Mon Oct 10 2011 at 14:10:02 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2181 !!! WARNING: LYS 209 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.946348 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): -22.03300 24.21200 ymin,ymax (A): -53.41900 -8.839001 zmin,zma (A): -34.72500 20.14700 x,y,z range (A): 46.24500 44.58000 54.87200 scale (grids/A): 1.946348 object centre (A): 1.089500 -31.12900 -7.288999 number of atom coordinates read : 2181 total number of charged atoms : 2040 net assigned charge : -7.271978 assigned positive charge : 327.6438 centred at (gu) : 88.02815 91.87894 94.71748 assigned negative charge : -334.9159 centred at (gu) : 88.12508 92.06535 95.07571 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66350 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20458 grid for indexing accessible points = 1.400000 m= 23037 mr = 44424 m= 3560 mr = 16469 m= 193 mr = 2168 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 30030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 16083 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) : 0.6487826 object centre at (A) : 1.089500 -31.12900 -7.288999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3426081E-02 -9.6439220E-02 midg,1,midg; midg,igrid,midg -1.2205556E-02 -2.0670267E-02 1,midg,midg; igrid,midg,midg 2.9223675E-03 -2.0442221E-03 gauss-seidel spectral radius is 0.9986539 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 14:10:04 rms-change max change #iterations 4.035749 180.4639 at 10iterations 1.891582 64.46607 at 20iterations 0.8895129 30.64971 at 30iterations 0.4180849 14.67172 at 40iterations 0.1957610 6.143933 at 50iterations 9.2157148E-02 2.947925 at 60iterations 4.3321218E-02 1.482887 at 70iterations 2.0340724E-02 0.6651487 at 80iterations 9.5834304E-03 0.3127928 at 90iterations 4.5086714E-03 0.1568623 at 100iterations 2.1222830E-03 6.9754601E-02 at 110iterations 9.9657732E-04 3.1076431E-02 at 120iterations finished qdiffx linear iterations at : 14:10:16 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 9.9657732E-04 3.1076431E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 14:10:17 13.409u 0.514s 0:14.37 96.7% 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 14:10:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2181 !!! WARNING: LYS 209 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.919522 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): -22.03300 24.21200 ymin,ymax (A): -53.41900 -8.839001 zmin,zma (A): -34.72500 20.14700 x,y,z range (A): 46.24500 44.58000 54.87200 scale (grids/A): 2.919522 object centre (A): 1.089500 -31.12900 -7.288999 number of atom coordinates read : 2181 total number of charged atoms : 2040 net assigned charge : -7.271978 assigned positive charge : 327.6438 centred at (gu) : 87.04220 92.81837 97.07625 assigned negative charge : -334.9159 centred at (gu) : 87.18755 93.09807 97.61353 start vw surface at 0.1100000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 153170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20458 grid for indexing accessible points = 1.400000 m= 74747 mr = 108006 m= 26456 mr = 59781 m= 6352 mr = 20866 m= 800 mr = 4698 m= 26 mr = 505 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.480000 number of dielectric boundary points 67689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 16319 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) : 1.946348 object centre at (A) : 1.089500 -31.12900 -7.288999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1841294 -1.120363 midg,1,midg; midg,igrid,midg -0.1252078 -0.1869201 1,midg,midg; igrid,midg,midg 3.9921455E-02 -1.6153380E-02 gauss-seidel spectral radius is 0.9992552 estimated iterations to convergence 289 setup time was (sec) 1.880000 now iterating at: 14:10:19 rms-change max change #iterations 9.374791 387.3097 at 10iterations 5.412835 114.3644 at 20iterations 3.106837 65.35321 at 30iterations 1.785637 36.16238 at 40iterations 1.025803 20.69672 at 50iterations 0.5878569 11.93626 at 60iterations 0.3367669 7.483908 at 70iterations 0.1930560 3.777925 at 80iterations 0.1103179 2.314323 at 90iterations 6.3244648E-02 1.381014 at 100iterations 3.6164805E-02 0.6975174 at 110iterations 2.0713186E-02 0.4028673 at 120iterations 1.1867813E-02 0.2328763 at 130iterations 6.7766672E-03 0.1284347 at 140iterations 3.8805492E-03 7.6525688E-02 at 150iterations 2.2275625E-03 4.1484952E-02 at 160iterations 1.2715288E-03 2.5627136E-02 at 170iterations 7.2959479E-04 1.5518188E-02 at 180iterations finished qdiffx linear iterations at : 14:10:39 total time elapsed so far: 22.20000 # loops : 180 mean,max change (kT/e) : 7.2959479E-04 1.5518188E-02 energy calculations done at 22.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.37000 DelPhi exited at 14:10:40 22.370u 0.534s 0:23.45 97.6% 0+0k 0+0io 0pf+0w