Sun Oct 9 21:09:36 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 Sun Oct 9 2011 at 21:09:36 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6063290 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): 44.16900 98.86400 ymin,ymax (A): 3.089000 61.80300 zmin,zma (A): 14.97200 67.49000 x,y,z range (A): 54.69500 58.71400 52.51800 scale (grids/A): 0.6063290 object centre (A): 71.51650 32.44600 41.23100 number of atom coordinates read : 3182 total number of charged atoms : 3126 net assigned charge : 8.025013 assigned positive charge : 499.3096 centred at (gu) : 90.86317 87.85841 90.48721 assigned negative charge : -491.2860 centred at (gu) : 90.79559 87.74644 90.51308 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8144 nv = 96 ne = 84 npr = 58156 no. pairs analyzed = 58156 no. exposed pairs = 4461 no. arc points = 33133 no. surface atoms = 1481 nbur = 1701 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3974 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3366 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 10164 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1684839E-09 3.1844167E-09 midg,1,midg; midg,igrid,midg -3.4710892E-09 6.5198136E-09 1,midg,midg; igrid,midg,midg 4.6405876E-10 9.7705666E-09 gauss-seidel spectral radius is 0.9859898 estimated iterations to convergence 69 setup time was (sec) 0.7000000 now iterating at: 21:09:38 rms-change max change #iterations 0.1265123 20.23223 at 10iterations 1.0877811E-02 1.852722 at 20iterations 9.5569331E-04 0.1522064 at 30iterations 8.6199179E-05 1.2224674E-02 at 40iterations 9.0541598E-06 1.1711121E-03 at 50iterations finished qdiffx linear iterations at : 21:09:42 total time elapsed so far: 5.180000 # loops : 50 mean,max change (kT/e) : 9.0541598E-06 1.1711121E-03 energy calculations done at 5.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.350000 DelPhi exited at 21:09:42 5.351u 0.460s 0:06.06 95.8% 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 21:09:43 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.818987 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): 44.16900 98.86400 ymin,ymax (A): 3.089000 61.80300 zmin,zma (A): 14.97200 67.49000 x,y,z range (A): 54.69500 58.71400 52.51800 scale (grids/A): 1.818987 object centre (A): 71.51650 32.44600 41.23100 number of atom coordinates read : 3182 total number of charged atoms : 3126 net assigned charge : 8.025013 assigned positive charge : 499.3096 centred at (gu) : 92.58865 83.57420 91.46091 assigned negative charge : -491.2860 centred at (gu) : 92.38641 83.23880 91.53876 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 87495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33133 grid for indexing accessible points = 1.400000 m= 28975 mr = 56691 m= 4162 mr = 19826 m= 248 mr = 2239 m= 3 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 239 time to turn everything in is 0.7600000 number of dielectric boundary points 42065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24397 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) : 0.6063290 object centre at (A) : 71.51650 32.44600 41.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7455774E-04 -9.4739487E-03 midg,1,midg; midg,igrid,midg 5.5971872E-02 6.9767244E-02 1,midg,midg; igrid,midg,midg 1.9440550E-03 1.6553430E-02 gauss-seidel spectral radius is 0.9985972 estimated iterations to convergence 212 setup time was (sec) 1.120000 now iterating at: 21:09:44 rms-change max change #iterations 4.409381 173.3300 at 10iterations 2.036531 65.86415 at 20iterations 0.9369899 29.58865 at 30iterations 0.4333906 14.91230 at 40iterations 0.1997970 6.255056 at 50iterations 9.2481866E-02 2.750202 at 60iterations 4.2766046E-02 1.263853 at 70iterations 1.9751497E-02 0.5599327 at 80iterations 9.1391550E-03 0.2672782 at 90iterations 4.2345780E-03 0.1462307 at 100iterations 1.9589062E-03 6.0829163E-02 at 110iterations 9.0616744E-04 2.9380798E-02 at 120iterations finished qdiffx linear iterations at : 21:09:56 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 9.0616744E-04 2.9380798E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.40000 DelPhi exited at 21:09:57 13.406u 0.513s 0:14.18 98.0% 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 Sun Oct 9 2011 at 21:09:57 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3182 !!! WARNING: SEP 139 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.728481 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): 44.16900 98.86400 ymin,ymax (A): 3.089000 61.80300 zmin,zma (A): 14.97200 67.49000 x,y,z range (A): 54.69500 58.71400 52.51800 scale (grids/A): 2.728481 object centre (A): 71.51650 32.44600 41.23100 number of atom coordinates read : 3182 total number of charged atoms : 3126 net assigned charge : 8.025013 assigned positive charge : 499.3096 centred at (gu) : 93.88286 80.36108 92.19121 assigned negative charge : -491.2860 centred at (gu) : 93.57961 79.85812 92.30806 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 202196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33133 grid for indexing accessible points = 1.400000 m= 95681 mr = 138714 m= 31637 mr = 74856 m= 7025 mr = 23766 m= 897 mr = 4830 m= 63 mr = 555 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 872 time to turn everything in is 1.950000 number of dielectric boundary points 94759 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.130000 number of grid points assigned charge 25004 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) : 1.818987 object centre at (A) : 71.51650 32.44600 41.23100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2743206E-02 -0.2061195 midg,1,midg; midg,igrid,midg 0.4968534 0.9725273 1,midg,midg; igrid,midg,midg 7.3101752E-02 0.1479468 gauss-seidel spectral radius is 0.9992790 estimated iterations to convergence 294 setup time was (sec) 2.370000 now iterating at: 21:10:00 rms-change max change #iterations 10.87706 345.8962 at 10iterations 6.557597 154.2280 at 20iterations 3.903374 85.98865 at 30iterations 2.301393 57.32664 at 40iterations 1.351544 27.45910 at 50iterations 0.7937687 16.84712 at 60iterations 0.4636299 10.08303 at 70iterations 0.2710262 4.656419 at 80iterations 0.1577381 3.077753 at 90iterations 9.1678254E-02 1.714240 at 100iterations 5.3377859E-02 0.9775391 at 110iterations 3.0985501E-02 0.5686932 at 120iterations 1.8003432E-02 0.3247738 at 130iterations 1.0433785E-02 0.2030414 at 140iterations 6.0500600E-03 0.1070442 at 150iterations 3.5085226E-03 6.2895775E-02 at 160iterations 2.0343098E-03 3.4479856E-02 at 170iterations 1.1767683E-03 2.2916794E-02 at 180iterations finished qdiffx linear iterations at : 21:10:20 total time elapsed so far: 22.84000 # loops : 180 mean,max change (kT/e) : 1.1767683E-03 2.2916794E-02 energy calculations done at 22.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.01000 DelPhi exited at 21:10:21 23.019u 0.530s 0:23.84 98.7% 0+0k 0+0io 0pf+0w