Tue Oct 11 07:36:00 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+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 Oct 11 2011 at 07:36:01 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3639 !!! WARNING: GLM 429 has a net charge of -0.0940 !!! WARNING: SEP 431 has a net charge of -0.4750 !!! WARNING: HIR 471 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5416014 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): 10.91300 61.30300 ymin,ymax (A): -1.091000 64.64000 zmin,zma (A): -1.001000 50.16800 x,y,z range (A): 50.39000 65.73100 51.16900 scale (grids/A): 0.5416014 object centre (A): 36.10800 31.77450 24.58350 number of atom coordinates read : 3639 total number of charged atoms : 3488 net assigned charge : -2.054981 assigned positive charge : 549.1125 centred at (gu) : 90.30677 90.56476 90.46172 assigned negative charge : -551.1697 centred at (gu) : 90.45104 90.63733 90.38738 start vw surface at 0.1800000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6944 nv = 96 ne = 84 npr = 74645 no. pairs analyzed = 74645 no. exposed pairs = 4099 no. arc points = 28105 no. surface atoms = 1401 nbur = 2238 mkacc time = 0.2500000 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 = 1.568000 m= 275 mr = 4016 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.4900000 number of dielectric boundary points 3197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 9091 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5814664E-10 4.6387164E-10 midg,1,midg; midg,igrid,midg 3.4597616E-10 -7.0834927E-10 1,midg,midg; igrid,midg,midg 8.2043428E-10 -1.2202157E-09 gauss-seidel spectral radius is 0.9824705 estimated iterations to convergence 62 setup time was (sec) 0.8400000 now iterating at: 07:36:02 rms-change max change #iterations 7.9669222E-02 11.34416 at 10iterations 6.0485834E-03 0.9357300 at 20iterations 7.8568183E-04 0.1444473 at 30iterations 1.7752612E-04 3.5060883E-02 at 40iterations 4.3609511E-05 8.8291168E-03 at 50iterations finished qdiffx linear iterations at : 07:36:05 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 4.3609511E-05 8.8291168E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 07:36:06 4.706u 0.400s 0:05.72 89.1% 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 Oct 11 2011 at 07:36:06 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3639 !!! WARNING: GLM 429 has a net charge of -0.0940 !!! WARNING: SEP 431 has a net charge of -0.4750 !!! WARNING: HIR 471 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.624804 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): 10.91300 61.30300 ymin,ymax (A): -1.091000 64.64000 zmin,zma (A): -1.001000 50.16800 x,y,z range (A): 50.39000 65.73100 51.16900 scale (grids/A): 1.624804 object centre (A): 36.10800 31.77450 24.58350 number of atom coordinates read : 3639 total number of charged atoms : 3488 net assigned charge : -2.054981 assigned positive charge : 549.1125 centred at (gu) : 90.91909 91.69334 91.38388 assigned negative charge : -551.1697 centred at (gu) : 91.35262 91.91167 91.16153 start vw surface at 0.1900000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 77224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26111 mr = 55556 m= 2666 mr = 19452 m= 64 mr = 1406 m= 0 mr = 9 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2480 time to turn everything in is 0.7700000 number of dielectric boundary points 29642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 26688 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) : 0.5416014 object centre at (A) : 36.10800 31.77450 24.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2758204E-02 -2.1216969E-03 midg,1,midg; midg,igrid,midg 1.5164214E-02 -1.7999839E-02 1,midg,midg; igrid,midg,midg 8.9965025E-03 -1.1448194E-02 gauss-seidel spectral radius is 0.9982288 estimated iterations to convergence 189 setup time was (sec) 1.090000 now iterating at: 07:36:08 rms-change max change #iterations 3.749329 157.2596 at 10iterations 1.579892 60.72315 at 20iterations 0.6678281 23.49029 at 30iterations 0.2812005 9.571218 at 40iterations 0.1196342 4.121265 at 50iterations 5.0373688E-02 1.641941 at 60iterations 2.1332163E-02 0.6998062 at 70iterations 9.0981228E-03 0.2911167 at 80iterations 3.9047427E-03 0.1402073 at 90iterations 1.6893260E-03 6.9303513E-02 at 100iterations 7.4254215E-04 2.6679993E-02 at 110iterations 3.3484207E-04 1.2248993E-02 at 120iterations finished qdiffx linear iterations at : 07:36:17 total time elapsed so far: 10.20000 # loops : 120 mean,max change (kT/e) : 3.3484207E-04 1.2248993E-02 energy calculations done at 10.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.41000 DelPhi exited at 07:36:18 10.417u 0.465s 0:11.34 95.8% 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 Tue Oct 11 2011 at 07:36:18 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3639 !!! WARNING: GLM 429 has a net charge of -0.0940 !!! WARNING: SEP 431 has a net charge of -0.4750 !!! WARNING: HIR 471 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.437206 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): 10.91300 61.30300 ymin,ymax (A): -1.091000 64.64000 zmin,zma (A): -1.001000 50.16800 x,y,z range (A): 50.39000 65.73100 51.16900 scale (grids/A): 2.437206 object centre (A): 36.10800 31.77450 24.58350 number of atom coordinates read : 3639 total number of charged atoms : 3488 net assigned charge : -2.054981 assigned positive charge : 549.1125 centred at (gu) : 91.37846 92.53992 92.07557 assigned negative charge : -551.1697 centred at (gu) : 92.02894 92.86745 91.74236 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 179420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 89786 mr = 134780 m= 26752 mr = 74454 m= 4239 mr = 21357 m= 328 mr = 2973 m= 5 mr = 152 m= 0 mr = 2 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 8179 time to turn everything in is 1.930000 number of dielectric boundary points 66812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 27854 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) : 1.624804 object centre at (A) : 36.10800 31.77450 24.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1559679 -1.2534039E-02 midg,1,midg; midg,igrid,midg 0.3680960 -0.4856704 1,midg,midg; igrid,midg,midg 0.1391530 -0.1610877 gauss-seidel spectral radius is 0.9991567 estimated iterations to convergence 272 setup time was (sec) 2.300000 now iterating at: 07:36:20 rms-change max change #iterations 9.487988 382.9567 at 10iterations 5.323029 113.6924 at 20iterations 2.979979 60.54675 at 30iterations 1.655628 37.85754 at 40iterations 0.9220634 18.19632 at 50iterations 0.5126916 9.400303 at 60iterations 0.2847525 5.591568 at 70iterations 0.1580428 2.971197 at 80iterations 8.7526657E-02 1.617076 at 90iterations 4.8561390E-02 0.9623299 at 100iterations 2.6941393E-02 0.5324478 at 110iterations 1.4937644E-02 0.2945490 at 120iterations 8.3027333E-03 0.1515503 at 130iterations 4.6335561E-03 8.3019257E-02 at 140iterations 2.5890956E-03 4.9942017E-02 at 150iterations 1.4611357E-03 2.7111053E-02 at 160iterations 8.3535223E-04 1.6963959E-02 at 170iterations 4.8586971E-04 9.7579956E-03 at 180iterations finished qdiffx linear iterations at : 07:36:36 total time elapsed so far: 17.65000 # loops : 180 mean,max change (kT/e) : 4.8586971E-04 9.7579956E-03 energy calculations done at 17.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.87000 DelPhi exited at 07:36:37 17.878u 0.465s 0:18.83 97.3% 0+0k 0+0io 0pf+0w