Wed Dec 21 14:21:14 PST 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 Wed Dec 21 2011 at 14:21:14 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 45 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 0.6108861 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): -9.125000 49.15100 ymin,ymax (A): 8.599000 47.76500 zmin,zma (A): -3.644000 38.79700 x,y,z range (A): 58.27600 39.16600 42.44100 scale (grids/A): 0.6108861 object centre (A): 20.01300 28.18200 17.57650 number of atom coordinates read : 1912 total number of charged atoms : 1780 net assigned charge : -3.839992 assigned positive charge : 282.1880 centred at (gu) : 90.05748 89.65556 90.53536 assigned negative charge : -286.0283 centred at (gu) : 90.09615 89.61932 90.61385 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4842 nv = 96 ne = 84 npr = 39786 no. pairs analyzed = 39786 no. exposed pairs = 2398 no. arc points = 16611 no. surface atoms = 809 nbur = 1103 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 196 mr = 2684 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2348 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1649 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 5826 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2632920E-10 -5.9410699E-09 midg,1,midg; midg,igrid,midg -3.9581565E-09 -8.9024665E-10 1,midg,midg; igrid,midg,midg -8.5354923E-10 -3.8081649E-09 gauss-seidel spectral radius is 0.9860677 estimated iterations to convergence 69 setup time was (sec) 0.4700000 now iterating at: 14:21:15 rms-change max change #iterations 0.1063761 18.16128 at 10iterations 9.2598218E-03 1.644341 at 20iterations 8.3168841E-04 0.1359806 at 30iterations 7.1594717E-05 1.1255264E-02 at 40iterations 6.3915054E-06 1.0452271E-03 at 50iterations finished qdiffx linear iterations at : 14:21:19 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 6.3915054E-06 1.0452271E-03 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 14:21:26 4.210u 0.436s 0:13.12 35.3% 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 Wed Dec 21 2011 at 14:21:30 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 45 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 1.832658 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): -9.125000 49.15100 ymin,ymax (A): 8.599000 47.76500 zmin,zma (A): -3.644000 38.79700 x,y,z range (A): 58.27600 39.16600 42.44100 scale (grids/A): 1.832658 object centre (A): 20.01300 28.18200 17.57650 number of atom coordinates read : 1912 total number of charged atoms : 1780 net assigned charge : -3.839992 assigned positive charge : 282.1880 centred at (gu) : 90.17233 88.96687 91.60596 assigned negative charge : -286.0283 centred at (gu) : 90.28874 88.85845 91.84153 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 52780 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16611 grid for indexing accessible points = 1.400000 m= 17660 mr = 36505 m= 2109 mr = 13135 m= 75 mr = 1222 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1446 time to turn everything in is 0.2800000 number of dielectric boundary points 21756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 13950 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) : 0.6108861 object centre at (A) : 20.01300 28.18200 17.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1696615E-04 -1.3267549E-02 midg,1,midg; midg,igrid,midg -2.1263142E-03 -2.2196297E-03 1,midg,midg; igrid,midg,midg 1.8534163E-02 1.4771099E-02 gauss-seidel spectral radius is 0.9984444 estimated iterations to convergence 201 setup time was (sec) 0.5000000 now iterating at: 14:21:32 rms-change max change #iterations 3.326956 144.1272 at 10iterations 1.474687 61.34248 at 20iterations 0.6553990 23.88732 at 30iterations 0.2927912 11.20070 at 40iterations 0.1300813 4.486922 at 50iterations 5.7622619E-02 2.081137 at 60iterations 2.5663730E-02 0.9848480 at 70iterations 1.1403905E-02 0.4367790 at 80iterations 5.0808769E-03 0.2277107 at 90iterations 2.2600633E-03 9.9947929E-02 at 100iterations 1.0088346E-03 4.3148041E-02 at 110iterations 4.4803179E-04 1.8305987E-02 at 120iterations finished qdiffx linear iterations at : 14:21:40 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 4.4803179E-04 1.8305987E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 14:21:50 8.008u 0.216s 0:20.50 40.0% 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 Wed Dec 21 2011 at 14:21:57 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1912 !!! WARNING: LYS 7 has a net charge of 0.0200 !!! WARNING: LYS 41 has a net charge of 0.0200 !!! WARNING: LYS 43 has a net charge of 0.0200 !!! WARNING: LYS 45 has a net charge of 0.0200 !!! WARNING: LYS 70 has a net charge of 0.0200 !!! WARNING: LYS 140 has a net charge of 0.0200 !!! WARNING: LYS 142 has a net charge of 0.0200 !!! WARNING: LYS 154 has a net charge of 0.0200 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: 2.748987 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): -9.125000 49.15100 ymin,ymax (A): 8.599000 47.76500 zmin,zma (A): -3.644000 38.79700 x,y,z range (A): 58.27600 39.16600 42.44100 scale (grids/A): 2.748987 object centre (A): 20.01300 28.18200 17.57650 number of atom coordinates read : 1912 total number of charged atoms : 1780 net assigned charge : -3.839992 assigned positive charge : 282.1880 centred at (gu) : 90.25860 88.45018 92.40895 assigned negative charge : -286.0283 centred at (gu) : 90.43317 88.28757 92.76238 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 122413 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16611 grid for indexing accessible points = 1.400000 m= 59754 mr = 88829 m= 18897 mr = 49087 m= 3465 mr = 15181 m= 289 mr = 2499 m= 6 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 4954 time to turn everything in is 0.6500000 number of dielectric boundary points 49106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14240 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) : 1.832658 object centre at (A) : 20.01300 28.18200 17.57650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1381462E-03 -0.1307751 midg,1,midg; midg,igrid,midg 1.3289830E-02 -1.8034698E-02 1,midg,midg; igrid,midg,midg 0.3127726 0.2678854 gauss-seidel spectral radius is 0.9991860 estimated iterations to convergence 277 setup time was (sec) 0.8800000 now iterating at: 14:21:59 rms-change max change #iterations 7.948798 281.5386 at 10iterations 4.481075 117.7535 at 20iterations 2.520756 55.32201 at 30iterations 1.410386 34.39995 at 40iterations 0.7893817 18.79950 at 50iterations 0.4413507 10.95191 at 60iterations 0.2457733 5.542841 at 70iterations 0.1372643 3.400040 at 80iterations 7.6593459E-02 1.778669 at 90iterations 4.2769916E-02 0.8887954 at 100iterations 2.3844454E-02 0.5670357 at 110iterations 1.3312532E-02 0.2945080 at 120iterations 7.4339053E-03 0.1611710 at 130iterations 4.1512116E-03 8.9323997E-02 at 140iterations 2.3120581E-03 5.3208590E-02 at 150iterations 1.2894142E-03 3.0236721E-02 at 160iterations 7.2161958E-04 1.5777588E-02 at 170iterations 4.0181860E-04 8.8853836E-03 at 180iterations finished qdiffx linear iterations at : 14:22:11 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 4.0181860E-04 8.8853836E-03 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 14:22:26 13.039u 0.234s 0:29.43 45.0% 0+0k 0+0io 0pf+0w