Sat Oct 8 11:34:27 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 11:34:27 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3345 !!! WARNING: HIR 14 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6373875 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): 31.25400 83.02400 ymin,ymax (A): 24.82200 80.67500 zmin,zma (A): -3.012000 47.34800 x,y,z range (A): 51.77000 55.85300 50.36000 scale (grids/A): 0.6373875 object centre (A): 57.13900 52.74850 22.16800 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.485962 assigned positive charge : 509.7534 centred at (gu) : 90.11972 89.63516 90.80900 assigned negative charge : -515.2404 centred at (gu) : 89.94402 89.71600 90.80783 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8781 nv = 96 ne = 84 npr = 70981 no. pairs analyzed = 70981 no. exposed pairs = 3739 no. arc points = 25500 no. surface atoms = 1264 nbur = 2081 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 5273 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 123 time to turn everything in is 0.3800000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4528338E-09 -8.6268086E-09 midg,1,midg; midg,igrid,midg 4.4688866E-09 -1.7772363E-08 1,midg,midg; igrid,midg,midg -3.2430844E-08 1.7862869E-08 gauss-seidel spectral radius is 0.9873000 estimated iterations to convergence 73 setup time was (sec) 0.6300000 now iterating at: 11:34:28 rms-change max change #iterations 0.1684187 23.85444 at 10iterations 1.6640404E-02 2.016677 at 20iterations 1.6672716E-03 0.2387199 at 30iterations 1.6381603E-04 2.2087097E-02 at 40iterations 1.6911230E-05 2.2811890E-03 at 50iterations finished qdiffx linear iterations at : 11:34:31 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 1.6911230E-05 2.2811890E-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) 3.610000 DelPhi exited at 11:34:31 3.616u 0.198s 0:04.15 91.5% 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 Sat Oct 8 2011 at 11:34:31 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3345 !!! WARNING: HIR 14 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.912162 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): 31.25400 83.02400 ymin,ymax (A): 24.82200 80.67500 zmin,zma (A): -3.012000 47.34800 x,y,z range (A): 51.77000 55.85300 50.36000 scale (grids/A): 1.912162 object centre (A): 57.13900 52.74850 22.16800 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.485962 assigned positive charge : 509.7534 centred at (gu) : 90.35826 88.90456 92.42608 assigned negative charge : -515.2404 centred at (gu) : 89.83158 89.14766 92.42274 start vw surface at 0.1700000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 95674 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25500 grid for indexing accessible points = 1.400000 m= 35543 mr = 69750 m= 5708 mr = 27421 m= 331 mr = 3912 m= 4 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 4488 time to turn everything in is 0.7100000 number of dielectric boundary points 36059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 25109 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) : 0.6373875 object centre at (A) : 57.13900 52.74850 22.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3623683E-02 -3.8223874E-02 midg,1,midg; midg,igrid,midg 1.7640132E-02 -3.0180812E-02 1,midg,midg; igrid,midg,midg -4.8870422E-02 4.0970328E-03 gauss-seidel spectral radius is 0.9987016 estimated iterations to convergence 220 setup time was (sec) 1.020000 now iterating at: 11:34:33 rms-change max change #iterations 5.006819 184.6515 at 10iterations 2.380384 74.71343 at 20iterations 1.139686 32.89919 at 30iterations 0.5447744 15.15671 at 40iterations 0.2600552 7.213640 at 50iterations 0.1244966 3.546028 at 60iterations 5.9543788E-02 1.603779 at 70iterations 2.8501417E-02 0.7945743 at 80iterations 1.3615399E-02 0.3998718 at 90iterations 6.5093841E-03 0.1866131 at 100iterations 3.1172566E-03 8.7585449E-02 at 110iterations 1.4899770E-03 4.0912628E-02 at 120iterations finished qdiffx linear iterations at : 11:34:40 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 1.4899770E-03 4.0912628E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 11:34:40 8.253u 0.224s 0:08.86 95.5% 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 Sat Oct 8 2011 at 11:34:40 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3345 !!! WARNING: HIR 14 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.868244 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): 31.25400 83.02400 ymin,ymax (A): 24.82200 80.67500 zmin,zma (A): -3.012000 47.34800 x,y,z range (A): 51.77000 55.85300 50.36000 scale (grids/A): 2.868244 object centre (A): 57.13900 52.74850 22.16800 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.485962 assigned positive charge : 509.7534 centred at (gu) : 90.53704 88.35647 93.63897 assigned negative charge : -515.2404 centred at (gu) : 89.74721 88.72119 93.63401 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 221602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25500 grid for indexing accessible points = 1.400000 m= 114657 mr = 167978 m= 42649 mr = 96623 m= 10462 mr = 35708 m= 1504 mr = 8226 m= 84 mr = 992 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 15280 time to turn everything in is 1.840000 number of dielectric boundary points 81393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 25543 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) : 1.912162 object centre at (A) : 57.13900 52.74850 22.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3265858 -0.3504362 midg,1,midg; midg,igrid,midg 0.2647317 0.1230282 1,midg,midg; igrid,midg,midg -0.5486785 -5.3867351E-02 gauss-seidel spectral radius is 0.9992794 estimated iterations to convergence 294 setup time was (sec) 2.180000 now iterating at: 11:34:43 rms-change max change #iterations 11.49721 363.5949 at 10iterations 6.743607 119.4255 at 20iterations 3.932924 86.08181 at 30iterations 2.285750 36.97025 at 40iterations 1.327357 22.27736 at 50iterations 0.7718069 12.51738 at 60iterations 0.4476041 7.415199 at 70iterations 0.2593134 3.868263 at 80iterations 0.1505883 2.348923 at 90iterations 8.7103166E-02 1.464449 at 100iterations 5.0420366E-02 0.9018936 at 110iterations 2.9215161E-02 0.4409409 at 120iterations 1.6909121E-02 0.2673416 at 130iterations 9.7956965E-03 0.1531658 at 140iterations 5.6817131E-03 8.9193344E-02 at 150iterations 3.2907801E-03 5.4679871E-02 at 160iterations 1.9055643E-03 2.9983521E-02 at 170iterations 1.1036245E-03 1.7721176E-02 at 180iterations finished qdiffx linear iterations at : 11:34:54 total time elapsed so far: 13.73000 # loops : 180 mean,max change (kT/e) : 1.1036245E-03 1.7721176E-02 energy calculations done at 13.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.93000 DelPhi exited at 11:34:55 13.935u 0.248s 0:14.54 97.4% 0+0k 0+0io 0pf+0w