Tue Oct 11 07:32:59 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 Tue Oct 11 2011 at 07:32:59 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3264 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5990140 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): 0.5429999 49.16300 ymin,ymax (A): -8.339000 49.48400 zmin,zma (A): 1.346000 60.77700 x,y,z range (A): 48.62000 57.82300 59.43100 scale (grids/A): 0.5990140 object centre (A): 24.85300 20.57250 31.06150 number of atom coordinates read : 3264 total number of charged atoms : 3093 net assigned charge : -0.5999887 assigned positive charge : 487.5659 centred at (gu) : 89.60139 89.40868 90.76905 assigned negative charge : -488.1669 centred at (gu) : 89.53165 89.35399 90.71648 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7710 nv = 96 ne = 84 npr = 67352 no. pairs analyzed = 67352 no. exposed pairs = 3918 no. arc points = 26301 no. surface atoms = 1341 nbur = 1923 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 4433 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2643 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9645 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1705941E-09 2.4995825E-09 midg,1,midg; midg,igrid,midg -3.0793397E-09 1.9015265E-09 1,midg,midg; igrid,midg,midg -3.6895758E-09 2.5900666E-09 gauss-seidel spectral radius is 0.9856262 estimated iterations to convergence 68 setup time was (sec) 0.7000000 now iterating at: 07:33:00 rms-change max change #iterations 0.1198869 18.74018 at 10iterations 1.2191250E-02 1.850304 at 20iterations 2.8689518E-03 0.4872208 at 30iterations 1.1477998E-03 0.2071037 at 40iterations 4.8588234E-04 8.7711334E-02 at 50iterations finished qdiffx linear iterations at : 07:33:03 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 4.8588234E-04 8.7711334E-02 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 07:33:04 4.208u 0.264s 0:05.06 88.1% 0+0k 0+0io 6pf+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 07:33:04 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3264 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.797042 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): 0.5429999 49.16300 ymin,ymax (A): -8.339000 49.48400 zmin,zma (A): 1.346000 60.77700 x,y,z range (A): 48.62000 57.82300 59.43100 scale (grids/A): 1.797042 object centre (A): 24.85300 20.57250 31.06150 number of atom coordinates read : 3264 total number of charged atoms : 3093 net assigned charge : -0.5999887 assigned positive charge : 487.5659 centred at (gu) : 88.80331 88.22557 92.30630 assigned negative charge : -488.1669 centred at (gu) : 88.59464 88.06160 92.14899 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 84875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26301 grid for indexing accessible points = 1.400000 m= 30814 mr = 60813 m= 4127 mr = 23188 m= 144 mr = 2519 m= 0 mr = 34 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1199 time to turn everything in is 0.7300000 number of dielectric boundary points 33406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24139 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) : 0.5990140 object centre at (A) : 24.85300 20.57250 31.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4834279E-02 -1.2863019E-03 midg,1,midg; midg,igrid,midg -1.3489337E-02 6.2474078E-03 1,midg,midg; igrid,midg,midg -7.5108693E-03 4.3900586E-03 gauss-seidel spectral radius is 0.9985331 estimated iterations to convergence 207 setup time was (sec) 1.040000 now iterating at: 07:33:05 rms-change max change #iterations 4.311551 162.2781 at 10iterations 1.964192 66.99579 at 20iterations 0.8966392 30.75714 at 30iterations 0.4110140 11.86745 at 40iterations 0.1883518 5.773661 at 50iterations 8.6440660E-02 2.445297 at 60iterations 3.9974254E-02 1.501995 at 70iterations 1.8946150E-02 0.6770267 at 80iterations 9.4399350E-03 0.3340225 at 90iterations 5.1064240E-03 0.1753311 at 100iterations 3.0942920E-03 0.1104927 at 110iterations 2.0802980E-03 8.0650330E-02 at 120iterations finished qdiffx linear iterations at : 07:33:14 total time elapsed so far: 9.590000 # loops : 120 mean,max change (kT/e) : 2.0802980E-03 8.0650330E-02 energy calculations done at 9.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.770000 DelPhi exited at 07:33:14 9.774u 0.328s 0:10.73 94.0% 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 07:33:15 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3264 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.695563 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): 0.5429999 49.16300 ymin,ymax (A): -8.339000 49.48400 zmin,zma (A): 1.346000 60.77700 x,y,z range (A): 48.62000 57.82300 59.43100 scale (grids/A): 2.695563 object centre (A): 24.85300 20.57250 31.06150 number of atom coordinates read : 3264 total number of charged atoms : 3093 net assigned charge : -0.5999887 assigned positive charge : 487.5659 centred at (gu) : 88.20462 87.33811 93.45930 assigned negative charge : -488.1669 centred at (gu) : 87.89175 87.09243 93.22359 start vw surface at 0.1700000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 196497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26301 grid for indexing accessible points = 1.400000 m= 101587 mr = 146998 m= 35007 mr = 84241 m= 7251 mr = 28597 m= 680 mr = 5375 m= 20 mr = 406 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 4005 time to turn everything in is 1.910000 number of dielectric boundary points 75425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 24743 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) : 1.797042 object centre at (A) : 24.85300 20.57250 31.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4500073 -0.1474185 midg,1,midg; midg,igrid,midg -0.3260928 0.1253906 1,midg,midg; igrid,midg,midg -7.8155667E-02 3.0836938E-02 gauss-seidel spectral radius is 0.9992418 estimated iterations to convergence 287 setup time was (sec) 2.260000 now iterating at: 07:33:17 rms-change max change #iterations 10.43253 328.0671 at 10iterations 6.089659 146.5390 at 20iterations 3.521968 68.88730 at 30iterations 2.036378 51.11123 at 40iterations 1.176628 25.48647 at 50iterations 0.6755207 12.10296 at 60iterations 0.3883254 6.941853 at 70iterations 0.2227532 4.030933 at 80iterations 0.1277112 2.210926 at 90iterations 7.3141530E-02 1.262329 at 100iterations 4.1993696E-02 0.7550621 at 110iterations 2.4138754E-02 0.4440098 at 120iterations 1.3997145E-02 0.2379608 at 130iterations 8.2150996E-03 0.1624184 at 140iterations 4.9462537E-03 0.1053238 at 150iterations 3.1203527E-03 7.1128845E-02 at 160iterations 2.1036004E-03 4.3071747E-02 at 170iterations 1.5245480E-03 3.4358978E-02 at 180iterations finished qdiffx linear iterations at : 07:33:31 total time elapsed so far: 16.54000 # loops : 180 mean,max change (kT/e) : 1.5245480E-03 3.4358978E-02 energy calculations done at 16.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.72000 DelPhi exited at 07:33:32 16.717u 0.331s 0:17.68 96.3% 0+0k 0+0io 0pf+0w