Sat Oct 8 16:23:33 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 Sat Oct 8 2011 at 16:23:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2408 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6572875 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): -21.48500 30.33700 ymin,ymax (A): 4.002000 50.17500 zmin,zma (A): -17.04500 37.11700 x,y,z range (A): 51.82200 46.17300 54.16199 scale (grids/A): 0.6572875 object centre (A): 4.426001 27.08850 10.03600 number of atom coordinates read : 2408 total number of charged atoms : 2349 net assigned charge : 6.500001 assigned positive charge : 361.4099 centred at (gu) : 90.20684 91.08361 90.39995 assigned negative charge : -354.9107 centred at (gu) : 90.26907 90.95410 90.41055 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7171 nv = 96 ne = 84 npr = 47626 no. pairs analyzed = 47626 no. exposed pairs = 3080 no. arc points = 21331 no. surface atoms = 1048 nbur = 1360 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3985 m= 6 mr = 70 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 0.2900000 number of dielectric boundary points 3545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2125 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8616 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5591780E-08 1.4439363E-08 midg,1,midg; midg,igrid,midg -5.4257199E-09 4.6004377E-08 1,midg,midg; igrid,midg,midg 2.4478739E-08 4.7202331E-09 gauss-seidel spectral radius is 0.9879909 estimated iterations to convergence 75 setup time was (sec) 0.5700000 now iterating at: 16:23:34 rms-change max change #iterations 0.1526586 23.63781 at 10iterations 1.5883474E-02 2.158305 at 20iterations 1.7733700E-03 0.2360334 at 30iterations 2.6190223E-04 3.7258625E-02 at 40iterations 6.3565727E-05 1.0030270E-02 at 50iterations finished qdiffx linear iterations at : 16:23:38 total time elapsed so far: 4.800000 # loops : 50 mean,max change (kT/e) : 6.3565727E-05 1.0030270E-02 energy calculations done at 4.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.990000 DelPhi exited at 16:23:38 4.990u 0.432s 0:05.67 95.5% 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 Sat Oct 8 2011 at 16:23:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2408 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.971862 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): -21.48500 30.33700 ymin,ymax (A): 4.002000 50.17500 zmin,zma (A): -17.04500 37.11700 x,y,z range (A): 51.82200 46.17300 54.16199 scale (grids/A): 1.971862 object centre (A): 4.426001 27.08850 10.03600 number of atom coordinates read : 2408 total number of charged atoms : 2349 net assigned charge : 6.500001 assigned positive charge : 361.4099 centred at (gu) : 90.61998 93.25024 91.19926 assigned negative charge : -354.9107 centred at (gu) : 90.80688 92.86207 91.23164 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 76942 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21331 grid for indexing accessible points = 1.400000 m= 28453 mr = 53649 m= 5138 mr = 21050 m= 408 mr = 3455 m= 10 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.7100000 number of dielectric boundary points 32646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 18583 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) : 0.6572875 object centre at (A) : 4.426001 27.08850 10.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9030772E-02 1.6150257E-02 midg,1,midg; midg,igrid,midg -9.6653221E-04 2.9485418E-02 1,midg,midg; igrid,midg,midg 1.5673647E-02 5.1056915E-03 gauss-seidel spectral radius is 0.9987092 estimated iterations to convergence 220 setup time was (sec) 1.040000 now iterating at: 16:23:40 rms-change max change #iterations 4.327631 165.0908 at 10iterations 2.066309 67.28039 at 20iterations 0.9848226 36.27787 at 30iterations 0.4741026 14.97657 at 40iterations 0.2263465 6.898165 at 50iterations 0.1087271 3.509300 at 60iterations 5.2116022E-02 1.698598 at 70iterations 2.4922391E-02 0.8570261 at 80iterations 1.1951213E-02 0.3649530 at 90iterations 5.7470030E-03 0.1771202 at 100iterations 2.7764272E-03 9.0782166E-02 at 110iterations 1.3445464E-03 4.2333603E-02 at 120iterations finished qdiffx linear iterations at : 16:23:51 total time elapsed so far: 12.19000 # loops : 120 mean,max change (kT/e) : 1.3445464E-03 4.2333603E-02 energy calculations done at 12.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.37000 DelPhi exited at 16:23:51 12.370u 0.486s 0:13.11 98.0% 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 Sat Oct 8 2011 at 16:23:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2408 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.957793 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): -21.48500 30.33700 ymin,ymax (A): 4.002000 50.17500 zmin,zma (A): -17.04500 37.11700 x,y,z range (A): 51.82200 46.17300 54.16199 scale (grids/A): 2.957793 object centre (A): 4.426001 27.08850 10.03600 number of atom coordinates read : 2408 total number of charged atoms : 2349 net assigned charge : 6.500001 assigned positive charge : 361.4099 centred at (gu) : 90.92976 94.87538 91.79880 assigned negative charge : -354.9107 centred at (gu) : 91.21033 94.29305 91.84744 start vw surface at 0.1000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 178211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21331 grid for indexing accessible points = 1.400000 m= 90391 mr = 130408 m= 34594 mr = 73799 m= 9743 mr = 28142 m= 1667 mr = 7595 m= 181 mr = 1158 m= 8 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 1.700000 number of dielectric boundary points 73604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 18792 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) : 1.971862 object centre at (A) : 4.426001 27.08850 10.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7643625E-02 0.1707292 midg,1,midg; midg,igrid,midg -2.9530857E-02 0.1732239 1,midg,midg; igrid,midg,midg 0.1580353 7.1155407E-02 gauss-seidel spectral radius is 0.9992812 estimated iterations to convergence 294 setup time was (sec) 2.070000 now iterating at: 16:23:54 rms-change max change #iterations 10.08081 491.3086 at 10iterations 5.954443 135.9736 at 20iterations 3.502254 81.32162 at 30iterations 2.057855 42.82455 at 40iterations 1.205069 24.11759 at 50iterations 0.7044819 14.90380 at 60iterations 0.4108069 7.435499 at 70iterations 0.2393930 4.464969 at 80iterations 0.1393678 2.699181 at 90iterations 8.0982298E-02 1.701578 at 100iterations 4.7062356E-02 0.8686471 at 110iterations 2.7366158E-02 0.4985428 at 120iterations 1.5870744E-02 0.2763262 at 130iterations 9.2538148E-03 0.1648750 at 140iterations 5.3691305E-03 0.1020513 at 150iterations 3.1298550E-03 5.6472301E-02 at 160iterations 1.8232008E-03 3.4771204E-02 at 170iterations 1.0674626E-03 2.0179031E-02 at 180iterations finished qdiffx linear iterations at : 16:24:13 total time elapsed so far: 20.69000 # loops : 180 mean,max change (kT/e) : 1.0674626E-03 2.0179031E-02 energy calculations done at 20.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.88000 DelPhi exited at 16:24:13 20.884u 0.519s 0:21.69 98.6% 0+0k 0+0io 0pf+0w