Mon Oct 10 14:11:57 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 14:11:57 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6353966 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): -4.142000 35.96800 ymin,ymax (A): -3.608000 49.53700 zmin,zma (A): -24.82200 31.20600 x,y,z range (A): 40.11000 53.14500 56.02800 scale (grids/A): 0.6353966 object centre (A): 15.91300 22.96450 3.192000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 90.22494 92.81767 90.32673 assigned negative charge : -287.6263 centred at (gu) : 90.31921 92.93625 90.26150 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5738 nv = 96 ne = 84 npr = 38360 no. pairs analyzed = 38360 no. exposed pairs = 2666 no. arc points = 18132 no. surface atoms = 902 nbur = 1062 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 371 mr = 3183 m= 0 mr = 68 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1822 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6484 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.9832968E-10 9.6213082E-09 midg,1,midg; midg,igrid,midg 7.0968178E-09 -9.5962323E-09 1,midg,midg; igrid,midg,midg 1.0595810E-08 -3.2698455E-09 gauss-seidel spectral radius is 0.9871201 estimated iterations to convergence 72 setup time was (sec) 0.4900000 now iterating at: 14:11:58 rms-change max change #iterations 0.1207494 20.00540 at 10iterations 1.1753724E-02 2.083071 at 20iterations 1.1357402E-03 0.1880188 at 30iterations 1.1136191E-04 1.8125534E-02 at 40iterations 1.0670912E-05 1.7967224E-03 at 50iterations finished qdiffx linear iterations at : 14:12:01 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.0670912E-05 1.7967224E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:12:01 3.422u 0.190s 0:04.07 88.6% 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 Mon Oct 10 2011 at 14:12:01 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.906190 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): -4.142000 35.96800 ymin,ymax (A): -3.608000 49.53700 zmin,zma (A): -24.82200 31.20600 x,y,z range (A): 40.11000 53.14500 56.02800 scale (grids/A): 1.906190 object centre (A): 15.91300 22.96450 3.192000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 90.67507 98.45300 90.98000 assigned negative charge : -287.6263 centred at (gu) : 90.95783 98.80893 90.78465 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 60257 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18132 grid for indexing accessible points = 1.400000 m= 25067 mr = 41256 m= 4893 mr = 19515 m= 274 mr = 3481 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 26142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 118 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 14418 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) : 0.6353966 object centre at (A) : 15.91300 22.96450 3.192000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6901586E-02 1.6118385E-02 midg,1,midg; midg,igrid,midg 3.0994359E-02 -9.4932467E-03 1,midg,midg; igrid,midg,midg 4.2279158E-03 -3.1775131E-03 gauss-seidel spectral radius is 0.9985682 estimated iterations to convergence 210 setup time was (sec) 0.8000000 now iterating at: 14:12:02 rms-change max change #iterations 3.584580 205.7724 at 10iterations 1.645724 86.64179 at 20iterations 0.7600113 29.64156 at 30iterations 0.3472215 11.96326 at 40iterations 0.1597612 5.625435 at 50iterations 7.3436439E-02 2.970905 at 60iterations 3.3640686E-02 1.150822 at 70iterations 1.5537921E-02 0.5755768 at 80iterations 7.1221092E-03 0.2868652 at 90iterations 3.2738533E-03 0.1176897 at 100iterations 1.5070733E-03 5.4725721E-02 at 110iterations 6.9419655E-04 2.3798943E-02 at 120iterations finished qdiffx linear iterations at : 14:12:09 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 6.9419655E-04 2.3798943E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:12:10 7.814u 0.212s 0:08.31 96.5% 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 14:12:10 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.859285 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): -4.142000 35.96800 ymin,ymax (A): -3.608000 49.53700 zmin,zma (A): -24.82200 31.20600 x,y,z range (A): 40.11000 53.14500 56.02800 scale (grids/A): 2.859285 object centre (A): 15.91300 22.96450 3.192000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 290.6260 centred at (gu) : 91.01260 102.6796 91.47014 assigned negative charge : -287.6263 centred at (gu) : 91.43679 103.2134 91.17696 start vw surface at 0.1400000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 138601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18132 grid for indexing accessible points = 1.400000 m= 76504 mr = 99356 m= 33072 mr = 63932 m= 9280 mr = 28091 m= 1367 mr = 7581 m= 67 mr = 959 m= 0 mr = 23 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 58949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 14656 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) : 1.906190 object centre at (A) : 15.91300 22.96450 3.192000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9369715 3.6254436E-02 midg,1,midg; midg,igrid,midg 0.3289129 -0.1437049 1,midg,midg; igrid,midg,midg 2.7767833E-02 -1.4091762E-02 gauss-seidel spectral radius is 0.9992280 estimated iterations to convergence 284 setup time was (sec) 1.560000 now iterating at: 14:12:11 rms-change max change #iterations 8.559257 377.4470 at 10iterations 4.928978 124.6960 at 20iterations 2.814039 67.79667 at 30iterations 1.604544 35.32507 at 40iterations 0.9149121 18.40169 at 50iterations 0.5204235 13.38038 at 60iterations 0.2961933 6.624680 at 70iterations 0.1680373 3.291069 at 80iterations 9.5472999E-02 2.086703 at 90iterations 5.4236408E-02 1.056511 at 100iterations 3.0707950E-02 0.6121311 at 110iterations 1.7431721E-02 0.3287420 at 120iterations 9.8814750E-03 0.2036867 at 130iterations 5.5993595E-03 0.1178192 at 140iterations 3.1749161E-03 7.4091911E-02 at 150iterations 1.8022171E-03 3.4515381E-02 at 160iterations 1.0211963E-03 1.9027710E-02 at 170iterations 5.7816826E-04 1.1547089E-02 at 180iterations finished qdiffx linear iterations at : 14:12:22 total time elapsed so far: 12.19000 # loops : 180 mean,max change (kT/e) : 5.7816826E-04 1.1547089E-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) 12.39000 DelPhi exited at 14:12:23 12.388u 0.230s 0:12.96 97.2% 0+0k 0+0io 0pf+0w