Tue Nov 22 14:11:41 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 Tue Nov 22 2011 at 14:11:46 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6412335 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): -5.799000 34.87400 ymin,ymax (A): -3.527000 48.80600 zmin,zma (A): -24.40700 31.11100 x,y,z range (A): 40.67300 52.33300 55.51800 scale (grids/A): 0.6412335 object centre (A): 14.53750 22.63950 3.352000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 90.79437 92.47195 90.18617 assigned negative charge : -288.0262 centred at (gu) : 90.89768 92.59928 90.13287 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5634 nv = 96 ne = 84 npr = 39807 no. pairs analyzed = 39807 no. exposed pairs = 2510 no. arc points = 17467 no. surface atoms = 843 nbur = 1121 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3142 m= 2 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2200000 number of dielectric boundary points 2746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6500 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3774000E-10 9.9830162E-09 midg,1,midg; midg,igrid,midg 9.5151238E-09 -1.1591291E-08 1,midg,midg; igrid,midg,midg 1.1787507E-08 -5.2660440E-09 gauss-seidel spectral radius is 0.9873450 estimated iterations to convergence 73 setup time was (sec) 0.4800000 now iterating at: 14:11:47 rms-change max change #iterations 0.1299836 19.18859 at 10iterations 1.3063838E-02 1.899149 at 20iterations 1.2628896E-03 0.2195129 at 30iterations 1.2506741E-04 2.0110130E-02 at 40iterations 1.2375254E-05 1.8148422E-03 at 50iterations finished qdiffx linear iterations at : 14:11:53 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.2375254E-05 1.8148422E-03 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 14:11:54 3.407u 0.221s 0:08.61 42.0% 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 Tue Nov 22 2011 at 14:11:55 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.923700 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): -5.799000 34.87400 ymin,ymax (A): -3.527000 48.80600 zmin,zma (A): -24.40700 31.11100 x,y,z range (A): 40.67300 52.33300 55.51800 scale (grids/A): 1.923700 object centre (A): 14.53750 22.63950 3.352000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 92.38313 97.41584 90.55855 assigned negative charge : -288.0262 centred at (gu) : 92.69319 97.79797 90.39867 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 59814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17467 grid for indexing accessible points = 1.400000 m= 22892 mr = 41324 m= 3843 mr = 17555 m= 208 mr = 2500 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2448 time to turn everything in is 0.4400000 number of dielectric boundary points 25294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14444 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) : 0.6412335 object centre at (A) : 14.53750 22.63950 3.352000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6190381E-02 1.1417226E-02 midg,1,midg; midg,igrid,midg 3.2885160E-02 -9.2288712E-03 1,midg,midg; igrid,midg,midg 7.6410240E-03 -4.5488668E-03 gauss-seidel spectral radius is 0.9985861 estimated iterations to convergence 211 setup time was (sec) 0.7200000 now iterating at: 14:11:57 rms-change max change #iterations 3.695998 174.2442 at 10iterations 1.706220 61.51199 at 20iterations 0.7912285 28.32332 at 30iterations 0.3646466 13.02967 at 40iterations 0.1679151 6.498306 at 50iterations 7.7585191E-02 2.816025 at 60iterations 3.5796855E-02 1.304257 at 70iterations 1.6514646E-02 0.5785007 at 80iterations 7.6291603E-03 0.2977676 at 90iterations 3.5264590E-03 0.1163397 at 100iterations 1.6331202E-03 5.8463573E-02 at 110iterations 7.5194909E-04 2.6644111E-02 at 120iterations finished qdiffx linear iterations at : 14:12:14 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 7.5194909E-04 2.6644111E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 14:12:16 7.760u 0.202s 0:20.86 38.1% 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 Nov 22 2011 at 14:12:17 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.885551 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): -5.799000 34.87400 ymin,ymax (A): -3.527000 48.80600 zmin,zma (A): -24.40700 31.11100 x,y,z range (A): 40.67300 52.33300 55.51800 scale (grids/A): 2.885551 object centre (A): 14.53750 22.63950 3.352000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 93.57471 101.1237 90.83797 assigned negative charge : -288.0262 centred at (gu) : 94.03973 101.6971 90.59811 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 138036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17467 grid for indexing accessible points = 1.400000 m= 72020 mr = 99638 m= 28485 mr = 60008 m= 7046 mr = 23728 m= 922 mr = 5467 m= 51 mr = 617 m= 0 mr = 15 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 8172 time to turn everything in is 1.110000 number of dielectric boundary points 57087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14655 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) : 1.923700 object centre at (A) : 14.53750 22.63950 3.352000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.079452 1.1326282E-02 midg,1,midg; midg,igrid,midg 0.3446442 -0.1430418 1,midg,midg; igrid,midg,midg 4.5260128E-02 -3.5960738E-02 gauss-seidel spectral radius is 0.9992319 estimated iterations to convergence 285 setup time was (sec) 1.450000 now iterating at: 14:12:23 rms-change max change #iterations 8.674394 348.3095 at 10iterations 4.999304 163.3484 at 20iterations 2.846740 74.98428 at 30iterations 1.625776 39.80943 at 40iterations 0.9285434 22.96571 at 50iterations 0.5293177 11.36557 at 60iterations 0.3009773 6.037209 at 70iterations 0.1711513 3.458269 at 80iterations 9.7503819E-02 2.013206 at 90iterations 5.5251606E-02 1.199402 at 100iterations 3.1445641E-02 0.6296449 at 110iterations 1.7861409E-02 0.3845910 at 120iterations 1.0129424E-02 0.2270355 at 130iterations 5.7576899E-03 0.1270971 at 140iterations 3.2688337E-03 6.2858582E-02 at 150iterations 1.8563225E-03 3.6648750E-02 at 160iterations 1.0551612E-03 2.2063255E-02 at 170iterations 5.9744267E-04 1.1632919E-02 at 180iterations finished qdiffx linear iterations at : 14:12:45 total time elapsed so far: 11.87000 # loops : 180 mean,max change (kT/e) : 5.9744267E-04 1.1632919E-02 energy calculations done at 11.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 14:12:47 12.041u 0.241s 0:30.31 40.5% 0+0k 0+0io 0pf+0w