Mon Oct 10 17:09:11 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 Mon Oct 10 2011 at 17:09:11 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3302 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: 0.5835970 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): 19.95700 76.28201 ymin,ymax (A): 26.94400 78.51000 zmin,zma (A): -22.99000 38.01100 x,y,z range (A): 56.32500 51.56600 61.00100 scale (grids/A): 0.5835970 object centre (A): 48.11950 52.72700 7.510501 number of atom coordinates read : 3302 total number of charged atoms : 3163 net assigned charge : 6.500014 assigned positive charge : 504.5348 centred at (gu) : 88.86284 89.74640 92.75735 assigned negative charge : -498.0358 centred at (gu) : 88.77243 89.78537 92.78139 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7387 nv = 96 ne = 84 npr = 66790 no. pairs analyzed = 66790 no. exposed pairs = 4185 no. arc points = 29551 no. surface atoms = 1398 nbur = 1904 mkacc time = 0.1100000 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 = 1.512000 m= 373 mr = 3921 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2400000 number of dielectric boundary points 3813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2928 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9336 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2362398E-09 1.8036163E-09 midg,1,midg; midg,igrid,midg 2.8698544E-09 5.3853422E-10 1,midg,midg; igrid,midg,midg -1.1659571E-09 3.1518890E-09 gauss-seidel spectral radius is 0.9848713 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 17:09:12 rms-change max change #iterations 0.1089414 16.29696 at 10iterations 8.7775951E-03 1.426687 at 20iterations 7.3198974E-04 0.1133411 at 30iterations 8.0974387E-05 1.6927719E-02 at 40iterations 1.4280458E-05 3.7231445E-03 at 50iterations finished qdiffx linear iterations at : 17:09:15 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.4280458E-05 3.7231445E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 17:09:16 3.563u 0.216s 0:05.06 74.5% 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 Mon Oct 10 2011 at 17:09:17 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3302 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: 1.750791 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): 19.95700 76.28201 ymin,ymax (A): 26.94400 78.51000 zmin,zma (A): -22.99000 38.01100 x,y,z range (A): 56.32500 51.56600 61.00100 scale (grids/A): 1.750791 object centre (A): 48.11950 52.72700 7.510501 number of atom coordinates read : 3302 total number of charged atoms : 3163 net assigned charge : 6.500014 assigned positive charge : 504.5348 centred at (gu) : 86.58799 89.23847 98.27124 assigned negative charge : -498.0358 centred at (gu) : 86.31678 89.35603 98.34370 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29551 grid for indexing accessible points = 1.400000 m= 27465 mr = 54408 m= 3536 mr = 19403 m= 136 mr = 1987 m= 0 mr = 30 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1258 time to turn everything in is 0.4100000 number of dielectric boundary points 35517 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 24533 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) : 0.5835970 object centre at (A) : 48.11950 52.72700 7.510501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9171940E-03 -1.2586357E-02 midg,1,midg; midg,igrid,midg 1.6800048E-02 1.2679322E-02 1,midg,midg; igrid,midg,midg 4.5615947E-03 2.6093129E-02 gauss-seidel spectral radius is 0.9984555 estimated iterations to convergence 202 setup time was (sec) 0.6500000 now iterating at: 17:09:17 rms-change max change #iterations 4.147171 153.4877 at 10iterations 1.839436 55.39254 at 20iterations 0.8188415 26.85793 at 30iterations 0.3662909 11.99027 at 40iterations 0.1627702 5.220021 at 50iterations 7.2650492E-02 2.334976 at 60iterations 3.2470748E-02 1.186872 at 70iterations 1.4472886E-02 0.4608994 at 80iterations 6.4815693E-03 0.2044144 at 90iterations 2.8840739E-03 0.1059675 at 100iterations 1.2940066E-03 3.8525581E-02 at 110iterations 5.7972787E-04 1.8449783E-02 at 120iterations finished qdiffx linear iterations at : 17:09:25 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 5.7972787E-04 1.8449783E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 17:09:25 8.256u 0.213s 0:08.93 94.7% 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 17:09:26 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3302 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: 2.626186 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): 19.95700 76.28201 ymin,ymax (A): 26.94400 78.51000 zmin,zma (A): -22.99000 38.01100 x,y,z range (A): 56.32500 51.56600 61.00100 scale (grids/A): 2.626186 object centre (A): 48.11950 52.72700 7.510501 number of atom coordinates read : 3302 total number of charged atoms : 3163 net assigned charge : 6.500014 assigned positive charge : 504.5348 centred at (gu) : 84.88181 88.85746 102.4067 assigned negative charge : -498.0358 centred at (gu) : 84.47501 89.03372 102.5155 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 185771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29551 grid for indexing accessible points = 1.400000 m= 90602 mr = 132403 m= 29933 mr = 72466 m= 5902 mr = 23243 m= 608 mr = 4140 m= 22 mr = 347 m= 0 mr = 2 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 4063 time to turn everything in is 1.000000 number of dielectric boundary points 80237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 25295 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) : 1.750791 object centre at (A) : 48.11950 52.72700 7.510501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0667885E-02 -7.8027725E-02 midg,1,midg; midg,igrid,midg 0.1945724 0.1857830 1,midg,midg; igrid,midg,midg -9.8571494E-02 0.3265367 gauss-seidel spectral radius is 0.9992275 estimated iterations to convergence 284 setup time was (sec) 1.250000 now iterating at: 17:09:27 rms-change max change #iterations 10.22096 259.4627 at 10iterations 5.918404 137.2812 at 20iterations 3.407176 69.45358 at 30iterations 1.948186 40.06370 at 40iterations 1.112179 22.30028 at 50iterations 0.6345239 13.09066 at 60iterations 0.3609130 6.841452 at 70iterations 0.2054051 3.668045 at 80iterations 0.1168234 2.392529 at 90iterations 6.6479594E-02 1.256887 at 100iterations 3.7652124E-02 0.6620808 at 110iterations 2.1388058E-02 0.3847427 at 120iterations 1.2145738E-02 0.2149038 at 130iterations 6.9045327E-03 0.1191721 at 140iterations 3.9116242E-03 7.4499130E-02 at 150iterations 2.2253308E-03 4.2370856E-02 at 160iterations 1.2675903E-03 2.6494503E-02 at 170iterations 7.2148500E-04 1.2942314E-02 at 180iterations finished qdiffx linear iterations at : 17:09:39 total time elapsed so far: 13.35000 # loops : 180 mean,max change (kT/e) : 7.2148500E-04 1.2942314E-02 energy calculations done at 13.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.48000 DelPhi exited at 17:09:40 13.478u 0.253s 0:14.07 97.5% 0+0k 0+0io 0pf+0w