Mon Oct 10 20:16:53 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 20:16:53 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 69 has a net charge of -0.0940 !!! WARNING: HIR 232 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6116523 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): -11.83900 45.29700 ymin,ymax (A): 30.16200 82.62000 zmin,zma (A): -12.82900 45.37400 x,y,z range (A): 57.13600 52.45800 58.20300 scale (grids/A): 0.6116523 object centre (A): 16.72900 56.39100 16.27250 number of atom coordinates read : 2589 total number of charged atoms : 2447 net assigned charge : -3.079988 assigned positive charge : 383.4169 centred at (gu) : 89.59852 90.58080 90.61732 assigned negative charge : -386.4979 centred at (gu) : 89.62537 90.68548 90.59187 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 51888 no. pairs analyzed = 51888 no. exposed pairs = 3606 no. arc points = 26116 no. surface atoms = 1208 nbur = 1381 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 3146 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3719 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2596 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7963 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.8050242E-09 -6.4902578E-10 midg,1,midg; midg,igrid,midg 3.0252996E-09 -8.4052409E-09 1,midg,midg; igrid,midg,midg -5.4351468E-10 -3.0078093E-09 gauss-seidel spectral radius is 0.9861744 estimated iterations to convergence 70 setup time was (sec) 0.4900000 now iterating at: 20:16:54 rms-change max change #iterations 0.1125425 20.31627 at 10iterations 9.8947044E-03 1.589190 at 20iterations 8.8430388E-04 0.1482635 at 30iterations 8.0906044E-05 1.3313293E-02 at 40iterations 8.2453462E-06 1.3113022E-03 at 50iterations finished qdiffx linear iterations at : 20:16:56 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 8.2453462E-06 1.3113022E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 20:16:57 3.132u 0.165s 0:03.93 83.7% 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 20:16:57 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 69 has a net charge of -0.0940 !!! WARNING: HIR 232 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.834957 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): -11.83900 45.29700 ymin,ymax (A): 30.16200 82.62000 zmin,zma (A): -12.82900 45.37400 x,y,z range (A): 57.13600 52.45800 58.20300 scale (grids/A): 1.834957 object centre (A): 16.72900 56.39100 16.27250 number of atom coordinates read : 2589 total number of charged atoms : 2447 net assigned charge : -3.079988 assigned positive charge : 383.4169 centred at (gu) : 88.79510 91.74205 91.85141 assigned negative charge : -386.4979 centred at (gu) : 88.87603 92.05624 91.77544 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 70000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26116 grid for indexing accessible points = 1.400000 m= 23445 mr = 45002 m= 3544 mr = 15933 m= 159 mr = 1906 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 34284 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 19191 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) : 0.6116523 object centre at (A) : 16.72900 56.39100 16.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3447357E-02 -3.7897483E-02 midg,1,midg; midg,igrid,midg 1.3909456E-02 -2.0638324E-02 1,midg,midg; igrid,midg,midg 1.5001258E-02 -1.8146597E-03 gauss-seidel spectral radius is 0.9985542 estimated iterations to convergence 209 setup time was (sec) 0.8200000 now iterating at: 20:16:58 rms-change max change #iterations 3.945524 177.6952 at 10iterations 1.788450 61.08189 at 20iterations 0.8192393 30.87520 at 30iterations 0.3742125 13.21176 at 40iterations 0.1708488 5.508783 at 50iterations 7.8016713E-02 2.699968 at 60iterations 3.5548750E-02 1.236015 at 70iterations 1.6286224E-02 0.5382347 at 80iterations 7.4665123E-03 0.2747660 at 90iterations 3.4075170E-03 0.1204224 at 100iterations 1.5591464E-03 5.3634644E-02 at 110iterations 7.1644242E-04 2.4612427E-02 at 120iterations finished qdiffx linear iterations at : 20:17:04 total time elapsed so far: 6.840000 # loops : 120 mean,max change (kT/e) : 7.1644242E-04 2.4612427E-02 energy calculations done at 6.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 20:17:05 7.025u 0.202s 0:07.78 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 Mon Oct 10 2011 at 20:17:05 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2589 !!! WARNING: GLM 69 has a net charge of -0.0940 !!! WARNING: HIR 232 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.752435 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): -11.83900 45.29700 ymin,ymax (A): 30.16200 82.62000 zmin,zma (A): -12.82900 45.37400 x,y,z range (A): 57.13600 52.45800 58.20300 scale (grids/A): 2.752435 object centre (A): 16.72900 56.39100 16.27250 number of atom coordinates read : 2589 total number of charged atoms : 2447 net assigned charge : -3.079988 assigned positive charge : 383.4169 centred at (gu) : 88.19240 92.61311 92.77698 assigned negative charge : -386.4979 centred at (gu) : 88.31401 93.08426 92.66325 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 161903 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26116 grid for indexing accessible points = 1.400000 m= 75854 mr = 110073 m= 26361 mr = 58957 m= 6139 mr = 20056 m= 667 mr = 4227 m= 11 mr = 287 m= 0 mr = 3 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 77332 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19574 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) : 1.834957 object centre at (A) : 16.72900 56.39100 16.27250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1141279 -0.3863202 midg,1,midg; midg,igrid,midg 0.1991707 -0.1431084 1,midg,midg; igrid,midg,midg 0.1851541 -6.2941551E-02 gauss-seidel spectral radius is 0.9992499 estimated iterations to convergence 288 setup time was (sec) 1.520000 now iterating at: 20:17:06 rms-change max change #iterations 9.658766 365.9576 at 10iterations 5.706664 149.3924 at 20iterations 3.333443 83.11481 at 30iterations 1.936191 43.71878 at 40iterations 1.119880 24.85063 at 50iterations 0.6481544 13.28518 at 60iterations 0.3731224 7.076402 at 70iterations 0.2145417 4.359758 at 80iterations 0.1229836 2.370857 at 90iterations 7.0586666E-02 1.506189 at 100iterations 4.0426522E-02 0.8093071 at 110iterations 2.3192225E-02 0.4690838 at 120iterations 1.3295837E-02 0.2672157 at 130iterations 7.6080966E-03 0.1386971 at 140iterations 4.3558846E-03 8.3075523E-02 at 150iterations 2.4924011E-03 4.6401024E-02 at 160iterations 1.4296998E-03 2.7496338E-02 at 170iterations 8.1938884E-04 1.6098976E-02 at 180iterations finished qdiffx linear iterations at : 20:17:16 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 8.1938884E-04 1.6098976E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 20:17:17 11.313u 0.193s 0:12.11 94.9% 0+0k 0+0io 0pf+0w