Sat Oct 15 14:27:58 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 Sat Oct 15 2011 at 14:27:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3193 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 0.5855552 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): -25.46700 32.33000 ymin,ymax (A): -8.966001 43.66600 zmin,zma (A): 6.851000 67.64800 x,y,z range (A): 57.79700 52.63200 60.79700 scale (grids/A): 0.5855552 object centre (A): 3.431499 17.35000 37.24950 number of atom coordinates read : 3193 total number of charged atoms : 3050 net assigned charge : -5.271958 assigned positive charge : 479.0895 centred at (gu) : 90.26298 88.64345 91.11827 assigned negative charge : -484.3629 centred at (gu) : 90.33771 88.49134 91.21918 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7232 nv = 96 ne = 84 npr = 63612 no. pairs analyzed = 63612 no. exposed pairs = 4145 no. arc points = 29163 no. surface atoms = 1401 nbur = 1792 mkacc time = 0.1100000 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= 341 mr = 3762 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2200000 number of dielectric boundary points 3790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2970 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2039667E-09 -5.4617479E-09 midg,1,midg; midg,igrid,midg -7.8690281E-09 2.1732884E-09 1,midg,midg; igrid,midg,midg 7.9309809E-10 -3.6532564E-09 gauss-seidel spectral radius is 0.9849668 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 14:27:58 rms-change max change #iterations 0.1038083 16.21633 at 10iterations 8.4035788E-03 1.449392 at 20iterations 6.7809015E-04 9.8482132E-02 at 30iterations 6.2629049E-05 1.0107040E-02 at 40iterations 9.0318481E-06 1.9922256E-03 at 50iterations finished qdiffx linear iterations at : 14:28:03 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 9.0318481E-06 1.9922256E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 14:28:04 3.537u 0.207s 0:06.30 59.2% 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 Sat Oct 15 2011 at 14:28:04 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 = 3193 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 1.756666 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): -25.46700 32.33000 ymin,ymax (A): -8.966001 43.66600 zmin,zma (A): 6.851000 67.64800 x,y,z range (A): 57.79700 52.63200 60.79700 scale (grids/A): 1.756666 object centre (A): 3.431499 17.35000 37.24950 number of atom coordinates read : 3193 total number of charged atoms : 3050 net assigned charge : -5.271958 assigned positive charge : 479.0895 centred at (gu) : 90.78751 85.92947 93.35370 assigned negative charge : -484.3629 centred at (gu) : 91.01269 85.47359 93.65723 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29163 grid for indexing accessible points = 1.400000 m= 25694 mr = 54054 m= 2949 mr = 17749 m= 109 mr = 1558 m= 4 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1211 time to turn everything in is 0.3900000 number of dielectric boundary points 35126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 23786 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) : 0.5855552 object centre at (A) : 3.431499 17.35000 37.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0165872E-02 9.8339906E-03 midg,1,midg; midg,igrid,midg -4.8803061E-02 4.0423819E-03 1,midg,midg; igrid,midg,midg 1.5759433E-02 -3.5530467E-02 gauss-seidel spectral radius is 0.9984621 estimated iterations to convergence 202 setup time was (sec) 0.6400000 now iterating at: 14:28:05 rms-change max change #iterations 4.069345 201.3382 at 10iterations 1.802202 67.59306 at 20iterations 0.8055561 28.08191 at 30iterations 0.3584415 12.51346 at 40iterations 0.1598297 5.278822 at 50iterations 7.1633898E-02 2.162928 at 60iterations 3.1978600E-02 1.118597 at 70iterations 1.4280854E-02 0.4310951 at 80iterations 6.3985097E-03 0.2009783 at 90iterations 2.8587696E-03 9.5829010E-02 at 100iterations 1.2783426E-03 4.3093681E-02 at 110iterations 5.7269668E-04 1.7926216E-02 at 120iterations finished qdiffx linear iterations at : 14:28:13 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 5.7269668E-04 1.7926216E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 14:28:13 8.450u 0.238s 0:08.98 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 15 2011 at 14:28:13 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 = 3193 !!! WARNING: GLN 355 has a net charge of -0.2720 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: 2.634998 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): -25.46700 32.33000 ymin,ymax (A): -8.966001 43.66600 zmin,zma (A): 6.851000 67.64800 x,y,z range (A): 57.79700 52.63200 60.79700 scale (grids/A): 2.634998 object centre (A): 3.431499 17.35000 37.24950 number of atom coordinates read : 3193 total number of charged atoms : 3050 net assigned charge : -5.271958 assigned positive charge : 479.0895 centred at (gu) : 91.18092 83.89414 95.03026 assigned negative charge : -484.3629 centred at (gu) : 91.51885 83.21024 95.48566 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29163 grid for indexing accessible points = 1.400000 m= 87168 mr = 131927 m= 26500 mr = 68860 m= 4864 mr = 20054 m= 509 mr = 3281 m= 15 mr = 305 m= 0 mr = 5 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 4356 time to turn everything in is 0.9900000 number of dielectric boundary points 79385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 24394 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) : 1.756666 object centre at (A) : 3.431499 17.35000 37.24950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6555163 0.2115649 midg,1,midg; midg,igrid,midg -0.6156688 5.8895163E-02 1,midg,midg; igrid,midg,midg 0.3433003 -0.3985954 gauss-seidel spectral radius is 0.9992328 estimated iterations to convergence 285 setup time was (sec) 1.240000 now iterating at: 14:28:15 rms-change max change #iterations 10.16152 263.7268 at 10iterations 5.935990 159.1360 at 20iterations 3.436242 80.89705 at 30iterations 1.983145 40.36863 at 40iterations 1.141737 22.25640 at 50iterations 0.6549429 15.80592 at 60iterations 0.3748707 8.100243 at 70iterations 0.2146279 4.464826 at 80iterations 0.1223461 2.372167 at 90iterations 6.9844760E-02 1.413269 at 100iterations 3.9825544E-02 0.7023485 at 110iterations 2.2671971E-02 0.4152279 at 120iterations 1.2920015E-02 0.2581917 at 130iterations 7.3540555E-03 0.1419239 at 140iterations 4.1936082E-03 8.1398010E-02 at 150iterations 2.3903854E-03 4.2678833E-02 at 160iterations 1.3602419E-03 2.5205612E-02 at 170iterations 7.7559717E-04 1.5594482E-02 at 180iterations finished qdiffx linear iterations at : 14:28:38 total time elapsed so far: 13.49000 # loops : 180 mean,max change (kT/e) : 7.7559717E-04 1.5594482E-02 energy calculations done at 13.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.62000 DelPhi exited at 14:28:38 13.620u 0.241s 0:25.11 55.1% 0+0k 0+0io 0pf+0w