Tue Oct 11 07:53:32 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 07:53:32 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6384276 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): -1.975000 53.78700 ymin,ymax (A): -22.76100 26.18600 zmin,zma (A): 9.101000 53.62900 x,y,z range (A): 55.76200 48.94700 44.52800 scale (grids/A): 0.6384276 object centre (A): 25.90600 1.712500 31.36500 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.411007 assigned positive charge : 360.2924 centred at (gu) : 88.84676 89.37154 90.26350 assigned negative charge : -353.8818 centred at (gu) : 88.83994 89.27471 90.04732 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6534 nv = 96 ne = 84 npr = 47866 no. pairs analyzed = 47866 no. exposed pairs = 2901 no. arc points = 20610 no. surface atoms = 984 nbur = 1396 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3631 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2070 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2783855E-08 3.2210725E-08 midg,1,midg; midg,igrid,midg -1.2303372E-09 1.6362890E-08 1,midg,midg; igrid,midg,midg 1.0487316E-08 7.6018205E-09 gauss-seidel spectral radius is 0.9872699 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 07:53:33 rms-change max change #iterations 0.1420868 20.36994 at 10iterations 1.4109842E-02 2.169941 at 20iterations 1.4598073E-03 0.2512398 at 30iterations 1.6386661E-04 2.5779724E-02 at 40iterations 2.1881420E-05 3.1814575E-03 at 50iterations finished qdiffx linear iterations at : 07:53:36 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 2.1881420E-05 3.1814575E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 07:53:37 4.047u 0.257s 0:04.59 93.4% 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 07:53:37 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.915283 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): -1.975000 53.78700 ymin,ymax (A): -22.76100 26.18600 zmin,zma (A): 9.101000 53.62900 x,y,z range (A): 55.76200 48.94700 44.52800 scale (grids/A): 1.915283 object centre (A): 25.90600 1.712500 31.36500 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.411007 assigned positive charge : 360.2924 centred at (gu) : 86.53996 88.11463 90.79021 assigned negative charge : -353.8818 centred at (gu) : 86.51977 87.82388 90.14181 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 70066 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20610 grid for indexing accessible points = 1.400000 m= 26424 mr = 48702 m= 3984 mr = 19794 m= 226 mr = 2437 m= 1 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 29676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17561 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) : 0.6384276 object centre at (A) : 25.90600 1.712500 31.36500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1577273E-02 4.1003786E-02 midg,1,midg; midg,igrid,midg -3.7846044E-03 8.5792979E-03 1,midg,midg; igrid,midg,midg 2.0856677E-02 3.2394268E-02 gauss-seidel spectral radius is 0.9986299 estimated iterations to convergence 214 setup time was (sec) 0.9400000 now iterating at: 07:53:38 rms-change max change #iterations 4.104731 183.9864 at 10iterations 1.913050 71.97626 at 20iterations 0.9032235 30.47394 at 30iterations 0.4218937 16.96765 at 40iterations 0.1978423 7.675743 at 50iterations 9.2649400E-02 3.267254 at 60iterations 4.3504599E-02 1.440029 at 70iterations 2.0348951E-02 0.6917801 at 80iterations 9.5266793E-03 0.3278245 at 90iterations 4.4805990E-03 0.1467781 at 100iterations 2.1025448E-03 7.0100784E-02 at 110iterations 9.8823011E-04 3.3358574E-02 at 120iterations finished qdiffx linear iterations at : 07:53:46 total time elapsed so far: 9.140000 # loops : 120 mean,max change (kT/e) : 9.8823011E-04 3.3358574E-02 energy calculations done at 9.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.310000 DelPhi exited at 07:53:47 9.315u 0.281s 0:09.88 97.0% 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 Oct 11 2011 at 07:53:47 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.872924 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): -1.975000 53.78700 ymin,ymax (A): -22.76100 26.18600 zmin,zma (A): 9.101000 53.62900 x,y,z range (A): 55.76200 48.94700 44.52800 scale (grids/A): 2.872924 object centre (A): 25.90600 1.712500 31.36500 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.411007 assigned positive charge : 360.2924 centred at (gu) : 84.80983 87.17176 91.18523 assigned negative charge : -353.8818 centred at (gu) : 84.77961 86.73582 90.21268 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 161763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20610 grid for indexing accessible points = 1.400000 m= 84341 mr = 117436 m= 31125 mr = 69948 m= 6989 mr = 25146 m= 1028 mr = 5154 m= 61 mr = 699 m= 0 mr = 30 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 66894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 17852 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) : 1.915283 object centre at (A) : 25.90600 1.712500 31.36500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2982386 0.4274623 midg,1,midg; midg,igrid,midg -5.3128362E-02 3.8233364E-03 1,midg,midg; igrid,midg,midg 8.0105208E-02 0.2740470 gauss-seidel spectral radius is 0.9992494 estimated iterations to convergence 288 setup time was (sec) 1.940000 now iterating at: 07:53:49 rms-change max change #iterations 9.546090 431.7086 at 10iterations 5.522567 140.9472 at 20iterations 3.194283 82.68107 at 30iterations 1.835319 37.26761 at 40iterations 1.055078 19.88528 at 50iterations 0.6057918 14.23815 at 60iterations 0.3474737 6.339123 at 70iterations 0.1989930 4.027531 at 80iterations 0.1139886 2.128138 at 90iterations 6.5325931E-02 1.305546 at 100iterations 3.7479181E-02 0.6820154 at 110iterations 2.1454966E-02 0.4003334 at 120iterations 1.2305938E-02 0.2431717 at 130iterations 7.0746867E-03 0.1408205 at 140iterations 4.0708277E-03 7.4217558E-02 at 150iterations 2.3553832E-03 4.6247482E-02 at 160iterations 1.3658490E-03 2.4932861E-02 at 170iterations 7.9976552E-04 1.4770508E-02 at 180iterations finished qdiffx linear iterations at : 07:54:02 total time elapsed so far: 15.32000 # loops : 180 mean,max change (kT/e) : 7.9976552E-04 1.4770508E-02 energy calculations done at 15.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.50000 DelPhi exited at 07:54:03 15.502u 0.311s 0:16.58 95.3% 0+0k 0+0io 0pf+0w