Sun Oct 9 05:19:10 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 Sun Oct 9 2011 at 05:19:10 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 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: 0.5736477 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): -32.72300 29.33600 ymin,ymax (A): -3.767000 45.13200 zmin,zma (A): -43.60300 17.05700 x,y,z range (A): 62.05900 48.89900 60.66000 scale (grids/A): 0.5736477 object centre (A): -1.693500 20.68250 -13.27300 number of atom coordinates read : 2769 total number of charged atoms : 2628 net assigned charge : 1.000016 assigned positive charge : 408.7022 centred at (gu) : 87.45985 89.39857 91.48515 assigned negative charge : -407.7034 centred at (gu) : 87.37859 89.46260 91.54918 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6073 nv = 96 ne = 84 npr = 55134 no. pairs analyzed = 55134 no. exposed pairs = 3616 no. arc points = 25403 no. surface atoms = 1217 nbur = 1552 mkacc time = 9.9999994E-02 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 = 1.484000 m= 310 mr = 3161 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 35 time to turn everything in is 0.2000000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2495 ## 285 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7681 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7678576E-10 -1.1793327E-09 midg,1,midg; midg,igrid,midg 1.4398573E-09 -7.0783995E-10 1,midg,midg; igrid,midg,midg -2.0611033E-09 8.3503743E-10 gauss-seidel spectral radius is 0.9843071 estimated iterations to convergence 66 setup time was (sec) 0.3800000 now iterating at: 05:19:10 rms-change max change #iterations 9.0720087E-02 13.20089 at 10iterations 6.8111275E-03 1.017906 at 20iterations 5.2926637E-04 8.4596634E-02 at 30iterations 4.4004701E-05 7.2174072E-03 at 40iterations 4.3341292E-06 7.0571899E-04 at 50iterations finished qdiffx linear iterations at : 05:19:13 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 4.3341292E-06 7.0571899E-04 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 05:19:13 3.344u 0.171s 0:03.78 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 Sun Oct 9 2011 at 05:19:13 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 = 2769 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: 1.720943 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): -32.72300 29.33600 ymin,ymax (A): -3.767000 45.13200 zmin,zma (A): -43.60300 17.05700 x,y,z range (A): 62.05900 48.89900 60.66000 scale (grids/A): 1.720943 object centre (A): -1.693500 20.68250 -13.27300 number of atom coordinates read : 2769 total number of charged atoms : 2628 net assigned charge : 1.000016 assigned positive charge : 408.7022 centred at (gu) : 82.37868 88.19486 94.45420 assigned negative charge : -407.7034 centred at (gu) : 82.13546 88.38739 94.64729 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66979 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25403 grid for indexing accessible points = 1.400000 m= 21991 mr = 45182 m= 2775 mr = 15423 m= 100 mr = 1493 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 928 time to turn everything in is 0.3400000 number of dielectric boundary points 29731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 231 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20405 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) : 0.5736477 object centre at (A) : -1.693500 20.68250 -13.27300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.0380829E-03 -4.6988423E-03 midg,1,midg; midg,igrid,midg 8.9104902E-03 -1.1327114E-03 1,midg,midg; igrid,midg,midg -2.5205219E-02 6.6839712E-04 gauss-seidel spectral radius is 0.9983530 estimated iterations to convergence 196 setup time was (sec) 0.5600000 now iterating at: 05:19:14 rms-change max change #iterations 3.531272 157.0477 at 10iterations 1.529308 59.79120 at 20iterations 0.6624172 22.89310 at 30iterations 0.2877664 9.625259 at 40iterations 0.1244428 4.742859 at 50iterations 5.4134041E-02 1.962763 at 60iterations 2.3544272E-02 0.7849731 at 70iterations 1.0208642E-02 0.3706541 at 80iterations 4.4369400E-03 0.1731911 at 90iterations 1.9284789E-03 7.0105076E-02 at 100iterations 8.4064249E-04 3.2548428E-02 at 110iterations 3.6601111E-04 1.4057159E-02 at 120iterations finished qdiffx linear iterations at : 05:19:21 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 3.6601111E-04 1.4057159E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 05:19:22 7.838u 0.196s 0:08.33 96.2% 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 Sun Oct 9 2011 at 05:19:22 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 = 2769 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: 2.581414 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): -32.72300 29.33600 ymin,ymax (A): -3.767000 45.13200 zmin,zma (A): -43.60300 17.05700 x,y,z range (A): 62.05900 48.89900 60.66000 scale (grids/A): 2.581414 object centre (A): -1.693500 20.68250 -13.27300 number of atom coordinates read : 2769 total number of charged atoms : 2628 net assigned charge : 1.000016 assigned positive charge : 408.7022 centred at (gu) : 78.56795 87.29214 96.68110 assigned negative charge : -407.7034 centred at (gu) : 78.20315 87.58108 96.97090 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 155443 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25403 grid for indexing accessible points = 1.400000 m= 73842 mr = 110579 m= 23463 mr = 58763 m= 4607 mr = 17928 m= 422 mr = 3265 m= 6 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 3266 time to turn everything in is 0.8200000 number of dielectric boundary points 67045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21017 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) : 1.720943 object centre at (A) : -1.693500 20.68250 -13.27300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1066561 -5.4345883E-02 midg,1,midg; midg,igrid,midg 9.7802527E-02 -6.0454472E-03 1,midg,midg; igrid,midg,midg -0.4987906 3.6814164E-02 gauss-seidel spectral radius is 0.9991867 estimated iterations to convergence 277 setup time was (sec) 1.040000 now iterating at: 05:19:23 rms-change max change #iterations 8.800751 286.5457 at 10iterations 5.005462 134.9228 at 20iterations 2.830201 55.74180 at 30iterations 1.591990 34.82808 at 40iterations 0.8936201 17.88370 at 50iterations 0.5016437 9.889097 at 60iterations 0.2817258 6.033079 at 70iterations 0.1575971 3.628866 at 80iterations 8.8138983E-02 1.792237 at 90iterations 4.9179465E-02 0.9781427 at 100iterations 2.7516324E-02 0.5533104 at 110iterations 1.5406980E-02 0.2980556 at 120iterations 8.6073363E-03 0.1925740 at 130iterations 4.8256000E-03 8.9830399E-02 at 140iterations 2.6893914E-03 5.7571411E-02 at 150iterations 1.5035846E-03 2.9507875E-02 at 160iterations 8.4098498E-04 2.1379471E-02 at 170iterations 4.7065699E-04 9.2563629E-03 at 180iterations finished qdiffx linear iterations at : 05:19:34 total time elapsed so far: 12.15000 # loops : 180 mean,max change (kT/e) : 4.7065699E-04 9.2563629E-03 energy calculations done at 12.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.29000 DelPhi exited at 05:19:35 12.295u 0.202s 0:12.76 97.8% 0+0k 0+0io 0pf+0w