Mon Oct 10 19:40:44 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+sph.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 = amb.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 Mon Oct 10 2011 at 19:40:44 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5849202 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): -11.45500 49.40800 ymin,ymax (A): -18.01400 39.76100 zmin,zma (A): -12.92300 46.20900 x,y,z range (A): 60.86300 57.77500 59.13200 scale (grids/A): 0.5849202 object centre (A): 18.97650 10.87350 16.64300 number of atom coordinates read : 3086 total number of charged atoms : 2944 net assigned charge : -1.499974 assigned positive charge : 463.0710 centred at (gu) : 87.78092 89.28899 90.69250 assigned negative charge : -464.5723 centred at (gu) : 87.77934 89.24609 90.73254 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6888 nv = 96 ne = 84 npr = 61859 no. pairs analyzed = 61859 no. exposed pairs = 4265 no. arc points = 30060 no. surface atoms = 1412 nbur = 1674 mkacc time = 0.1600000 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 = 1.456000 m= 371 mr = 3341 m= 0 mr = 22 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2892 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9460215E-10 -1.7024977E-09 midg,1,midg; midg,igrid,midg -1.8022581E-09 6.5669825E-10 1,midg,midg; igrid,midg,midg -6.7980255E-10 -1.9930958E-10 gauss-seidel spectral radius is 0.9849287 estimated iterations to convergence 67 setup time was (sec) 0.6800000 now iterating at: 19:40:46 rms-change max change #iterations 0.1038168 20.84592 at 10iterations 8.3159423E-03 1.389877 at 20iterations 6.9108361E-04 0.1178157 at 30iterations 7.4419717E-05 1.2783051E-02 at 40iterations 1.5458503E-05 2.6512146E-03 at 50iterations finished qdiffx linear iterations at : 19:40:50 total time elapsed so far: 4.910000 # loops : 50 mean,max change (kT/e) : 1.5458503E-05 2.6512146E-03 energy calculations done at 4.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.070000 DelPhi exited at 19:40:50 5.077u 0.437s 0:05.80 94.8% 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 Mon Oct 10 2011 at 19:40:50 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.754761 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): -11.45500 49.40800 ymin,ymax (A): -18.01400 39.76100 zmin,zma (A): -12.92300 46.20900 x,y,z range (A): 60.86300 57.77500 59.13200 scale (grids/A): 1.754761 object centre (A): 18.97650 10.87350 16.64300 number of atom coordinates read : 3086 total number of charged atoms : 2944 net assigned charge : -1.499974 assigned positive charge : 463.0710 centred at (gu) : 83.34176 87.86597 92.07648 assigned negative charge : -464.5723 centred at (gu) : 83.33775 87.73812 92.19735 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74968 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30060 grid for indexing accessible points = 1.400000 m= 24240 mr = 48613 m= 3250 mr = 16132 m= 123 mr = 1620 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.6600000 number of dielectric boundary points 36209 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22846 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) : 0.5849202 object centre at (A) : 18.97650 10.87350 16.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8679715E-03 -2.9186670E-02 midg,1,midg; midg,igrid,midg 5.5782520E-03 1.5459143E-02 1,midg,midg; igrid,midg,midg 6.0807741E-03 3.8386371E-03 gauss-seidel spectral radius is 0.9984564 estimated iterations to convergence 202 setup time was (sec) 1.040000 now iterating at: 19:40:52 rms-change max change #iterations 4.010454 160.6270 at 10iterations 1.773041 62.36854 at 20iterations 0.7926939 29.24406 at 30iterations 0.3518415 12.00963 at 40iterations 0.1564884 6.059349 at 50iterations 6.9738820E-02 2.292603 at 60iterations 3.1162225E-02 0.9938087 at 70iterations 1.3888166E-02 0.5028324 at 80iterations 6.2332558E-03 0.2012701 at 90iterations 2.7677671E-03 9.2805862E-02 at 100iterations 1.2433848E-03 4.2724609E-02 at 110iterations 5.5386784E-04 1.9085884E-02 at 120iterations finished qdiffx linear iterations at : 19:41:03 total time elapsed so far: 12.13000 # loops : 120 mean,max change (kT/e) : 5.5386784E-04 1.9085884E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.31000 DelPhi exited at 19:41:03 12.310u 0.481s 0:13.16 97.1% 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 Mon Oct 10 2011 at 19:41:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3086 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.632141 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): -11.45500 49.40800 ymin,ymax (A): -18.01400 39.76100 zmin,zma (A): -12.92300 46.20900 x,y,z range (A): 60.86300 57.77500 59.13200 scale (grids/A): 2.632141 object centre (A): 18.97650 10.87350 16.64300 number of atom coordinates read : 3086 total number of charged atoms : 2944 net assigned charge : -1.499974 assigned positive charge : 463.0710 centred at (gu) : 80.01249 86.79890 93.11447 assigned negative charge : -464.5723 centred at (gu) : 80.00657 86.60710 93.29600 start vw surface at 0.1400000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 173650 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30060 grid for indexing accessible points = 1.400000 m= 79768 mr = 119305 m= 26436 mr = 61488 m= 5235 mr = 19443 m= 458 mr = 3393 m= 16 mr = 185 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 1064 time to turn everything in is 1.640000 number of dielectric boundary points 81750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 23544 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) : 1.754761 object centre at (A) : 18.97650 10.87350 16.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9972724E-02 -0.3691739 midg,1,midg; midg,igrid,midg 0.1057880 0.2755192 1,midg,midg; igrid,midg,midg 0.2039886 2.2342883E-02 gauss-seidel spectral radius is 0.9992293 estimated iterations to convergence 284 setup time was (sec) 2.010000 now iterating at: 19:41:06 rms-change max change #iterations 9.955067 273.3496 at 10iterations 5.840170 171.9634 at 20iterations 3.393865 91.63113 at 30iterations 1.955613 43.44550 at 40iterations 1.126444 23.63932 at 50iterations 0.6461945 14.33762 at 60iterations 0.3696504 10.35694 at 70iterations 0.2110793 4.113346 at 80iterations 0.1203799 2.426714 at 90iterations 6.8654612E-02 1.248596 at 100iterations 3.9080683E-02 0.7532310 at 110iterations 2.2258516E-02 0.4476089 at 120iterations 1.2674758E-02 0.2456243 at 130iterations 7.1986290E-03 0.1403770 at 140iterations 4.1050422E-03 7.4010849E-02 at 150iterations 2.3418549E-03 4.5715332E-02 at 160iterations 1.3342715E-03 2.6260376E-02 at 170iterations 7.6544168E-04 1.5573502E-02 at 180iterations finished qdiffx linear iterations at : 19:41:24 total time elapsed so far: 20.45000 # loops : 180 mean,max change (kT/e) : 7.6544168E-04 1.5573502E-02 energy calculations done at 20.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.61000 DelPhi exited at 19:41:25 20.615u 0.523s 0:21.62 97.7% 0+0k 0+0io 0pf+0w