Sat Oct 8 21:55:05 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 Sat Oct 8 2011 at 21:55:05 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIR 88 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6321135 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): -8.729000 43.87300 ymin,ymax (A): -21.39500 34.92400 zmin,zma (A): 2.973000 54.90400 x,y,z range (A): 52.60200 56.31900 51.93100 scale (grids/A): 0.6321135 object centre (A): 17.57200 6.764500 28.93850 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.514003 assigned positive charge : 392.9519 centred at (gu) : 88.77225 89.34080 91.81025 assigned negative charge : -388.4384 centred at (gu) : 88.82393 89.28210 91.71086 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7028 nv = 96 ne = 84 npr = 51977 no. pairs analyzed = 51977 no. exposed pairs = 3340 no. arc points = 23621 no. surface atoms = 1116 nbur = 1477 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3731 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2387 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8479 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8881684E-09 2.1061664E-08 midg,1,midg; midg,igrid,midg -6.6267780E-10 9.0659773E-09 1,midg,midg; igrid,midg,midg 1.2763674E-08 1.5939651E-10 gauss-seidel spectral radius is 0.9870386 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 21:55:06 rms-change max change #iterations 0.1409213 22.78093 at 10iterations 1.3380229E-02 2.162510 at 20iterations 1.3027716E-03 0.1876945 at 30iterations 1.3297146E-04 2.3870468E-02 at 40iterations 2.1260961E-05 3.0274391E-03 at 50iterations finished qdiffx linear iterations at : 21:55:09 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.1260961E-05 3.0274391E-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) 3.550000 DelPhi exited at 21:55:09 3.555u 0.191s 0:04.03 92.8% 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 Sat Oct 8 2011 at 21:55:10 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIR 88 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.896340 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): -8.729000 43.87300 ymin,ymax (A): -21.39500 34.92400 zmin,zma (A): 2.973000 54.90400 x,y,z range (A): 52.60200 56.31900 51.93100 scale (grids/A): 1.896340 object centre (A): 17.57200 6.764500 28.93850 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.514003 assigned positive charge : 392.9519 centred at (gu) : 86.31623 88.02183 95.43056 assigned negative charge : -388.4384 centred at (gu) : 86.47153 87.84605 95.13220 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23621 grid for indexing accessible points = 1.400000 m= 26674 mr = 51470 m= 4175 mr = 19018 m= 254 mr = 2517 m= 3 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 33297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19315 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) : 0.6321135 object centre at (A) : 17.57200 6.764500 28.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9656256E-02 2.4601581E-02 midg,1,midg; midg,igrid,midg -3.1197470E-02 1.3354964E-02 1,midg,midg; igrid,midg,midg 2.2558255E-02 1.7331164E-02 gauss-seidel spectral radius is 0.9986294 estimated iterations to convergence 214 setup time was (sec) 0.6100000 now iterating at: 21:55:10 rms-change max change #iterations 4.278121 174.6773 at 10iterations 2.006087 66.05102 at 20iterations 0.9436333 27.88495 at 30iterations 0.4418809 14.36469 at 40iterations 0.2066958 6.551998 at 50iterations 9.7007304E-02 3.324371 at 60iterations 4.5236543E-02 1.367614 at 70iterations 2.1205120E-02 0.7160816 at 80iterations 9.9041834E-03 0.3121758 at 90iterations 4.6577961E-03 0.1504631 at 100iterations 2.1808094E-03 7.0795059E-02 at 110iterations 1.0191861E-03 3.3140182E-02 at 120iterations finished qdiffx linear iterations at : 21:55:18 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 1.0191861E-03 3.3140182E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.330000 DelPhi exited at 21:55:18 8.331u 0.239s 0:08.86 96.6% 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 Sat Oct 8 2011 at 21:55:18 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2593 !!! WARNING: HIR 88 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.844511 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): -8.729000 43.87300 ymin,ymax (A): -21.39500 34.92400 zmin,zma (A): 2.973000 54.90400 x,y,z range (A): 52.60200 56.31900 51.93100 scale (grids/A): 2.844511 object centre (A): 17.57200 6.764500 28.93850 number of atom coordinates read : 2593 total number of charged atoms : 2453 net assigned charge : 4.514003 assigned positive charge : 392.9519 centred at (gu) : 84.47437 87.03263 98.14560 assigned negative charge : -388.4384 centred at (gu) : 84.70719 86.76896 97.69825 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 174601 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23621 grid for indexing accessible points = 1.400000 m= 86849 mr = 125567 m= 30568 mr = 69987 m= 7449 mr = 23760 m= 1160 mr = 5416 m= 73 mr = 783 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.5599999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 75150 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 19622 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) : 1.896340 object centre at (A) : 17.57200 6.764500 28.93850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3039634 0.2650756 midg,1,midg; midg,igrid,midg -0.7656435 0.1290089 1,midg,midg; igrid,midg,midg 0.3626792 9.7350746E-02 gauss-seidel spectral radius is 0.9992685 estimated iterations to convergence 292 setup time was (sec) 1.250000 now iterating at: 21:55:20 rms-change max change #iterations 10.18488 381.4215 at 10iterations 6.066407 142.8207 at 20iterations 3.585799 78.06464 at 30iterations 2.111559 47.31968 at 40iterations 1.233161 24.56028 at 50iterations 0.7220029 14.92268 at 60iterations 0.4203598 7.747971 at 70iterations 0.2443108 4.504333 at 80iterations 0.1414976 2.580404 at 90iterations 8.2057588E-02 1.524864 at 100iterations 4.7456853E-02 0.8388963 at 110iterations 2.7483568E-02 0.4878755 at 120iterations 1.5881933E-02 0.2844419 at 130iterations 9.1672121E-03 0.1609068 at 140iterations 5.2965647E-03 0.1186314 at 150iterations 3.0599323E-03 6.0757637E-02 at 160iterations 1.7624571E-03 3.3492088E-02 at 170iterations 1.0203286E-03 1.9279480E-02 at 180iterations finished qdiffx linear iterations at : 21:55:32 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 1.0203286E-03 1.9279480E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 21:55:32 13.573u 0.220s 0:14.06 98.0% 0+0k 0+0io 0pf+0w