Sun Oct 9 21:03:32 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 Sun Oct 9 2011 at 21:03:33 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: SEP 158 has a net charge of -0.4750 !!! WARNING: CYS 277 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6312729 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): -39.93800 16.45600 ymin,ymax (A): -11.97100 31.89200 zmin,zma (A): -17.28300 36.23900 x,y,z range (A): 56.39400 43.86300 53.52200 scale (grids/A): 0.6312729 object centre (A): -11.74100 9.960501 9.478001 number of atom coordinates read : 2499 total number of charged atoms : 2354 net assigned charge : 4.525007 assigned positive charge : 376.9690 centred at (gu) : 91.46381 89.01947 90.14560 assigned negative charge : -372.4446 centred at (gu) : 91.53534 88.97456 90.08313 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6469 nv = 96 ne = 84 npr = 51023 no. pairs analyzed = 51023 no. exposed pairs = 3098 no. arc points = 21998 no. surface atoms = 1048 nbur = 1451 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3442 m= 6 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.3100000 number of dielectric boundary points 3330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8004 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6068966E-10 1.1015219E-08 midg,1,midg; midg,igrid,midg 1.5175452E-09 7.4273592E-09 1,midg,midg; igrid,midg,midg 8.3786391E-09 -1.6268220E-09 gauss-seidel spectral radius is 0.9869925 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 21:03:33 rms-change max change #iterations 0.1337653 20.11831 at 10iterations 1.2812556E-02 2.304187 at 20iterations 1.2309086E-03 0.2207489 at 30iterations 1.1729469E-04 1.6582489E-02 at 40iterations 1.1222462E-05 1.6422272E-03 at 50iterations finished qdiffx linear iterations at : 21:03:36 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 1.1222462E-05 1.6422272E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 21:03:36 3.376u 0.147s 0:03.79 92.6% 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 21:03:36 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: SEP 158 has a net charge of -0.4750 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 1.893819 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): -39.93800 16.45600 ymin,ymax (A): -11.97100 31.89200 zmin,zma (A): -17.28300 36.23900 x,y,z range (A): 56.39400 43.86300 53.52200 scale (grids/A): 1.893819 object centre (A): -11.74100 9.960501 9.478001 number of atom coordinates read : 2499 total number of charged atoms : 2354 net assigned charge : 4.525007 assigned positive charge : 376.9690 centred at (gu) : 94.39094 87.05782 90.43650 assigned negative charge : -372.4446 centred at (gu) : 94.60598 86.92355 90.24918 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 70261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 23245 mr = 47492 m= 3548 mr = 16589 m= 224 mr = 2177 m= 3 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1449 time to turn everything in is 0.5200000 number of dielectric boundary points 30917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18510 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) : 0.6312729 object centre at (A) : -11.74100 9.960501 9.478001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6815439E-02 2.3204442E-02 midg,1,midg; midg,igrid,midg -1.7078066E-02 -2.6448043E-03 1,midg,midg; igrid,midg,midg 4.5670774E-02 -6.1224669E-04 gauss-seidel spectral radius is 0.9986032 estimated iterations to convergence 212 setup time was (sec) 0.8000000 now iterating at: 21:03:37 rms-change max change #iterations 4.062960 164.4436 at 10iterations 1.872630 67.90686 at 20iterations 0.8675866 29.01413 at 30iterations 0.4032089 13.57096 at 40iterations 0.1867167 6.299870 at 50iterations 8.6744845E-02 3.170681 at 60iterations 4.0088907E-02 1.215484 at 70iterations 1.8621184E-02 0.6227169 at 80iterations 8.6458093E-03 0.3101845 at 90iterations 4.0003480E-03 0.1390233 at 100iterations 1.8612216E-03 5.9219360E-02 at 110iterations 8.6337904E-04 2.9638290E-02 at 120iterations finished qdiffx linear iterations at : 21:03:45 total time elapsed so far: 8.230000 # loops : 120 mean,max change (kT/e) : 8.6337904E-04 2.9638290E-02 energy calculations done at 8.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 21:03:45 8.438u 0.167s 0:08.87 96.8% 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 21:03:45 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: SEP 158 has a net charge of -0.4750 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 2.840728 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): -39.93800 16.45600 ymin,ymax (A): -11.97100 31.89200 zmin,zma (A): -17.28300 36.23900 x,y,z range (A): 56.39400 43.86300 53.52200 scale (grids/A): 2.840728 object centre (A): -11.74100 9.960501 9.478001 number of atom coordinates read : 2499 total number of charged atoms : 2354 net assigned charge : 4.525007 assigned positive charge : 376.9690 centred at (gu) : 96.58641 85.58656 90.65459 assigned negative charge : -372.4446 centred at (gu) : 96.90883 85.38523 90.37367 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 162735 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21998 grid for indexing accessible points = 1.400000 m= 76482 mr = 115736 m= 26035 mr = 61419 m= 6314 mr = 20371 m= 1039 mr = 4705 m= 65 mr = 753 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 4956 time to turn everything in is 1.270000 number of dielectric boundary points 69664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18828 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) : 1.893819 object centre at (A) : -11.74100 9.960501 9.478001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2310143 0.1918186 midg,1,midg; midg,igrid,midg -0.1390759 -5.4252360E-02 1,midg,midg; igrid,midg,midg 0.5016933 -7.4621156E-02 gauss-seidel spectral radius is 0.9992480 estimated iterations to convergence 288 setup time was (sec) 1.580000 now iterating at: 21:03:47 rms-change max change #iterations 9.499225 325.1553 at 10iterations 5.483402 118.6544 at 20iterations 3.141915 62.64512 at 30iterations 1.799890 39.39029 at 40iterations 1.029468 19.60750 at 50iterations 0.5875424 11.07663 at 60iterations 0.3364038 6.192385 at 70iterations 0.1922112 3.736601 at 80iterations 0.1097833 2.224180 at 90iterations 6.2693216E-02 1.262217 at 100iterations 3.5845265E-02 0.7056160 at 110iterations 2.0395901E-02 0.3754692 at 120iterations 1.1667155E-02 0.2257047 at 130iterations 6.6576474E-03 0.1303992 at 140iterations 3.8041975E-03 6.6635132E-02 at 150iterations 2.1741316E-03 3.8934708E-02 at 160iterations 1.2403118E-03 2.3242950E-02 at 170iterations 7.0984371E-04 1.4153957E-02 at 180iterations finished qdiffx linear iterations at : 21:03:57 total time elapsed so far: 11.68000 # loops : 180 mean,max change (kT/e) : 7.0984371E-04 1.4153957E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 21:03:58 11.866u 0.177s 0:12.31 97.7% 0+0k 0+0io 0pf+0w