Sun Oct 9 01:50:36 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 Sun Oct 9 2011 at 01:50:37 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2360 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6343211 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): -27.22500 28.09300 ymin,ymax (A): 8.160999 50.14400 zmin,zma (A): -12.78600 43.33700 x,y,z range (A): 55.31800 41.98300 56.12300 scale (grids/A): 0.6343211 object centre (A): 0.4340000 29.15250 15.27550 number of atom coordinates read : 2360 total number of charged atoms : 2226 net assigned charge : 11.51402 assigned positive charge : 344.7305 centred at (gu) : 90.49615 91.08453 91.13618 assigned negative charge : -333.2171 centred at (gu) : 90.42174 91.07529 91.08729 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6680 nv = 96 ne = 84 npr = 46166 no. pairs analyzed = 46166 no. exposed pairs = 3219 no. arc points = 23055 no. surface atoms = 1070 nbur = 1290 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3411 m= 0 mr = 26 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2206 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7764 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8600246E-09 2.3220208E-08 midg,1,midg; midg,igrid,midg 1.0633284E-08 1.8682538E-08 1,midg,midg; igrid,midg,midg 6.9572343E-09 2.2662489E-08 gauss-seidel spectral radius is 0.9871165 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 01:50:37 rms-change max change #iterations 0.1299946 21.06986 at 10iterations 1.2298337E-02 1.828350 at 20iterations 1.2125527E-03 0.1888418 at 30iterations 1.2188433E-04 2.0863533E-02 at 40iterations 1.2338156E-05 1.7032623E-03 at 50iterations finished qdiffx linear iterations at : 01:50:40 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 1.2338156E-05 1.7032623E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 01:50:41 3.609u 0.192s 0:04.06 93.3% 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 Sun Oct 9 2011 at 01:50:41 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2360 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.902963 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): -27.22500 28.09300 ymin,ymax (A): 8.160999 50.14400 zmin,zma (A): -12.78600 43.33700 x,y,z range (A): 55.31800 41.98300 56.12300 scale (grids/A): 1.902963 object centre (A): 0.4340000 29.15250 15.27550 number of atom coordinates read : 2360 total number of charged atoms : 2226 net assigned charge : 11.51402 assigned positive charge : 344.7305 centred at (gu) : 91.48832 93.25327 93.40806 assigned negative charge : -333.2171 centred at (gu) : 91.26535 93.22574 93.26201 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23055 grid for indexing accessible points = 1.400000 m= 24819 mr = 46897 m= 3910 mr = 17408 m= 257 mr = 2222 m= 6 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 354 time to turn everything in is 0.3700000 number of dielectric boundary points 33205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17478 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) : 0.6343211 object centre at (A) : 0.4340000 29.15250 15.27550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6080807E-02 2.7204087E-02 midg,1,midg; midg,igrid,midg 4.1962444E-04 2.7919568E-02 1,midg,midg; igrid,midg,midg 2.5801172E-02 5.0526384E-02 gauss-seidel spectral radius is 0.9986231 estimated iterations to convergence 214 setup time was (sec) 0.6000000 now iterating at: 01:50:41 rms-change max change #iterations 3.978140 169.3403 at 10iterations 1.843668 69.51786 at 20iterations 0.8594881 29.08541 at 30iterations 0.3986991 14.14229 at 40iterations 0.1857831 5.849097 at 50iterations 8.6509280E-02 2.769548 at 60iterations 4.0278267E-02 1.259373 at 70iterations 1.8792396E-02 0.5977321 at 80iterations 8.7686097E-03 0.2854965 at 90iterations 4.0747817E-03 0.1391945 at 100iterations 1.9074590E-03 6.3583374E-02 at 110iterations 8.8798476E-04 2.9193878E-02 at 120iterations finished qdiffx linear iterations at : 01:50:49 total time elapsed so far: 8.220000 # loops : 120 mean,max change (kT/e) : 8.8798476E-04 2.9193878E-02 energy calculations done at 8.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 01:50:50 8.354u 0.221s 0:08.94 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 Sun Oct 9 2011 at 01:50:50 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2360 !!! WARNING: HIT 84 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.854445 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): -27.22500 28.09300 ymin,ymax (A): 8.160999 50.14400 zmin,zma (A): -12.78600 43.33700 x,y,z range (A): 55.31800 41.98300 56.12300 scale (grids/A): 2.854445 object centre (A): 0.4340000 29.15250 15.27550 number of atom coordinates read : 2360 total number of charged atoms : 2226 net assigned charge : 11.51402 assigned positive charge : 344.7305 centred at (gu) : 92.23249 94.87984 95.11211 assigned negative charge : -333.2171 centred at (gu) : 91.89815 94.83862 94.89306 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23055 grid for indexing accessible points = 1.400000 m= 80090 mr = 114165 m= 28682 mr = 63690 m= 6911 mr = 22113 m= 1020 mr = 4811 m= 73 mr = 632 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1168 time to turn everything in is 0.9100000 number of dielectric boundary points 74957 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17804 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) : 1.902963 object centre at (A) : 0.4340000 29.15250 15.27550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5687807 0.2424298 midg,1,midg; midg,igrid,midg -2.2121575E-02 0.2976095 1,midg,midg; igrid,midg,midg 0.2085127 0.5518508 gauss-seidel spectral radius is 0.9992638 estimated iterations to convergence 291 setup time was (sec) 1.170000 now iterating at: 01:50:51 rms-change max change #iterations 9.400171 379.9215 at 10iterations 5.541073 136.1430 at 20iterations 3.234415 80.41159 at 30iterations 1.889061 43.29346 at 40iterations 1.100585 23.69640 at 50iterations 0.6376120 12.12297 at 60iterations 0.3685763 7.694660 at 70iterations 0.2133645 4.264256 at 80iterations 0.1234354 2.457087 at 90iterations 7.1016297E-02 1.414520 at 100iterations 4.1049019E-02 0.8437080 at 110iterations 2.3583118E-02 0.4628735 at 120iterations 1.3584536E-02 0.2700157 at 130iterations 7.8176586E-03 0.1455336 at 140iterations 4.5025414E-03 9.3305230E-02 at 150iterations 2.5887978E-03 4.5004368E-02 at 160iterations 1.4928556E-03 3.2989502E-02 at 170iterations 8.5791637E-04 1.5804291E-02 at 180iterations finished qdiffx linear iterations at : 01:51:03 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 8.5791637E-04 1.5804291E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 01:51:03 13.335u 0.253s 0:13.88 97.8% 0+0k 0+0io 0pf+0w