Tue Oct 11 06:02:46 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 Tue Oct 11 2011 at 06:02:46 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7241955 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): 25.88100 72.78300 ymin,ymax (A): -18.57800 30.58000 zmin,zma (A): 3.918000 46.56900 x,y,z range (A): 46.90200 49.15800 42.65100 scale (grids/A): 0.7241955 object centre (A): 49.33200 6.001000 25.24350 number of atom coordinates read : 2320 total number of charged atoms : 1990 net assigned charge : 5.945010 assigned positive charge : 325.9259 centred at (gu) : 89.13984 90.46336 90.31907 assigned negative charge : -319.9810 centred at (gu) : 89.28118 90.39111 90.40276 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7583 nv = 96 ne = 84 npr = 42653 no. pairs analyzed = 42653 no. exposed pairs = 2566 no. arc points = 17436 no. surface atoms = 876 nbur = 1444 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 530 mr = 4419 m= 4 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1629 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8215 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2572320E-07 1.1692665E-08 midg,1,midg; midg,igrid,midg 1.8415143E-08 1.3677904E-07 1,midg,midg; igrid,midg,midg 2.0602685E-07 -2.6233065E-08 gauss-seidel spectral radius is 0.9900597 estimated iterations to convergence 82 setup time was (sec) 0.3700000 now iterating at: 06:02:46 rms-change max change #iterations 0.2217831 28.99709 at 10iterations 2.9492043E-02 3.984919 at 20iterations 4.1923383E-03 0.4901047 at 30iterations 7.3100312E-04 9.0187073E-02 at 40iterations 1.9216423E-04 2.1951675E-02 at 50iterations finished qdiffx linear iterations at : 06:02:49 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.9216423E-04 2.1951675E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 06:02:50 3.342u 0.155s 0:03.92 89.0% 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 Tue Oct 11 2011 at 06:02:50 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.172586 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): 25.88100 72.78300 ymin,ymax (A): -18.57800 30.58000 zmin,zma (A): 3.918000 46.56900 x,y,z range (A): 46.90200 49.15800 42.65100 scale (grids/A): 2.172586 object centre (A): 49.33200 6.001000 25.24350 number of atom coordinates read : 2320 total number of charged atoms : 1990 net assigned charge : 5.945010 assigned positive charge : 325.9259 centred at (gu) : 87.41960 91.39003 90.95724 assigned negative charge : -319.9810 centred at (gu) : 87.84348 91.17342 91.20827 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 79743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17436 grid for indexing accessible points = 1.400000 m= 33684 mr = 57125 m= 7035 mr = 25980 m= 729 mr = 4844 m= 21 mr = 392 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 32869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15815 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) : 0.7241955 object centre at (A) : 49.33200 6.001000 25.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3231769E-02 3.3790536E-02 midg,1,midg; midg,igrid,midg 4.1631218E-02 3.6720090E-02 1,midg,midg; igrid,midg,midg 5.0794523E-02 -6.3887686E-02 gauss-seidel spectral radius is 0.9988796 estimated iterations to convergence 236 setup time was (sec) 0.6100000 now iterating at: 06:02:50 rms-change max change #iterations 4.865751 188.0153 at 10iterations 2.450325 81.77699 at 20iterations 1.237587 39.58760 at 30iterations 0.6218053 19.13257 at 40iterations 0.3138861 9.800455 at 50iterations 0.1577447 4.329696 at 60iterations 7.9823099E-02 2.433922 at 70iterations 4.0125124E-02 1.242843 at 80iterations 2.0448754E-02 0.6378918 at 90iterations 1.0412911E-02 0.3785439 at 100iterations 5.3061233E-03 0.1433430 at 110iterations 2.7665598E-03 8.4220886E-02 at 120iterations finished qdiffx linear iterations at : 06:02:57 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.7665598E-03 8.4220886E-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) 7.750000 DelPhi exited at 06:02:58 7.756u 0.206s 0:08.26 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 Tue Oct 11 2011 at 06:02:58 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.258880 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): 25.88100 72.78300 ymin,ymax (A): -18.57800 30.58000 zmin,zma (A): 3.918000 46.56900 x,y,z range (A): 46.90200 49.15800 42.65100 scale (grids/A): 3.258880 object centre (A): 49.33200 6.001000 25.24350 number of atom coordinates read : 2320 total number of charged atoms : 1990 net assigned charge : 5.945010 assigned positive charge : 325.9259 centred at (gu) : 86.12940 92.08511 91.43580 assigned negative charge : -319.9810 centred at (gu) : 86.76521 91.76013 91.81237 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 183402 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17436 grid for indexing accessible points = 1.400000 m= 102626 mr = 136906 m= 44403 mr = 86217 m= 13676 mr = 37082 m= 2951 mr = 10821 m= 402 mr = 2201 m= 22 mr = 278 m= 0 mr = 3 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 73974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 15920 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) : 2.172586 object centre at (A) : 49.33200 6.001000 25.24350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1128833 0.2745759 midg,1,midg; midg,igrid,midg 0.3257807 0.2217778 1,midg,midg; igrid,midg,midg 0.4998457 -0.7258751 gauss-seidel spectral radius is 0.9993088 estimated iterations to convergence 300 setup time was (sec) 1.500000 now iterating at: 06:03:00 rms-change max change #iterations 10.72778 424.2926 at 10iterations 6.366824 119.2753 at 20iterations 3.776447 69.92489 at 30iterations 2.238161 48.54822 at 40iterations 1.324384 25.18979 at 50iterations 0.7809479 13.26502 at 60iterations 0.4603487 8.732498 at 70iterations 0.2718543 4.454596 at 80iterations 0.1601508 2.827385 at 90iterations 9.4217613E-02 1.684944 at 100iterations 5.5756349E-02 1.004829 at 110iterations 3.3020657E-02 0.5507364 at 120iterations 1.9747468E-02 0.3626442 at 130iterations 1.1977247E-02 0.2019386 at 140iterations 7.4949451E-03 0.1434784 at 150iterations 4.8537059E-03 0.1016922 at 160iterations 3.3110373E-03 6.0264587E-02 at 170iterations 2.3987514E-03 4.3548584E-02 at 180iterations finished qdiffx linear iterations at : 06:03:11 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.3987514E-03 4.3548584E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 06:03:11 12.871u 0.197s 0:13.39 97.5% 0+0k 0+0io 0pf+0w