Sat Oct 8 23:55:24 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 8 2011 at 23:55:24 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 = 2444 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: 0.6399194 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): -12.74300 40.71000 ymin,ymax (A): -30.41900 25.21300 zmin,zma (A): -9.639000 33.90500 x,y,z range (A): 53.45300 55.63200 43.54400 scale (grids/A): 0.6399194 object centre (A): 13.98350 -2.603000 12.13300 number of atom coordinates read : 2444 total number of charged atoms : 2309 net assigned charge : 11.50002 assigned positive charge : 355.3571 centred at (gu) : 89.69943 91.07087 90.30610 assigned negative charge : -343.8579 centred at (gu) : 89.66963 91.08218 90.24442 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6799 nv = 96 ne = 84 npr = 49248 no. pairs analyzed = 49248 no. exposed pairs = 3175 no. arc points = 23283 no. surface atoms = 1058 nbur = 1386 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 3585 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2100000 number of dielectric boundary points 3608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2222 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8140 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6852002E-09 2.4530598E-08 midg,1,midg; midg,igrid,midg 1.4319720E-08 1.9374983E-08 1,midg,midg; igrid,midg,midg 1.4471374E-08 1.8554047E-08 gauss-seidel spectral radius is 0.9873422 estimated iterations to convergence 73 setup time was (sec) 0.4100000 now iterating at: 23:55:24 rms-change max change #iterations 0.1397159 20.62294 at 10iterations 1.3918253E-02 2.045080 at 20iterations 1.4981589E-03 0.2055645 at 30iterations 2.5817531E-04 4.4471741E-02 at 40iterations 7.5078438E-05 1.4774323E-02 at 50iterations finished qdiffx linear iterations at : 23:55:27 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 7.5078438E-05 1.4774323E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 23:55:28 3.578u 0.181s 0:04.10 91.4% 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 23:55:28 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 = 2444 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: 1.919758 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): -12.74300 40.71000 ymin,ymax (A): -30.41900 25.21300 zmin,zma (A): -9.639000 33.90500 x,y,z range (A): 53.45300 55.63200 43.54400 scale (grids/A): 1.919758 object centre (A): 13.98350 -2.603000 12.13300 number of atom coordinates read : 2444 total number of charged atoms : 2309 net assigned charge : 11.50002 assigned positive charge : 355.3571 centred at (gu) : 89.09781 93.21221 90.91786 assigned negative charge : -343.8579 centred at (gu) : 89.00905 93.24658 90.73329 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73225 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23283 grid for indexing accessible points = 1.400000 m= 25812 mr = 49367 m= 4197 mr = 18406 m= 265 mr = 2517 m= 2 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 2617 time to turn everything in is 0.3800000 number of dielectric boundary points 33120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18173 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) : 0.6399194 object centre at (A) : 13.98350 -2.603000 12.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0185605E-03 2.2721071E-02 midg,1,midg; midg,igrid,midg 4.0459048E-02 3.4160707E-02 1,midg,midg; igrid,midg,midg 4.9564425E-02 4.8614062E-02 gauss-seidel spectral radius is 0.9986510 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 23:55:29 rms-change max change #iterations 4.045181 173.3839 at 10iterations 1.895655 66.48419 at 20iterations 0.8919241 30.45988 at 30iterations 0.4182366 13.93177 at 40iterations 0.1967248 6.129532 at 50iterations 9.2433199E-02 2.882075 at 60iterations 4.3424439E-02 1.326431 at 70iterations 2.0498140E-02 0.6612854 at 80iterations 9.6621504E-03 0.3005829 at 90iterations 4.5915889E-03 0.1633947 at 100iterations 2.2016356E-03 7.0283890E-02 at 110iterations 1.0816276E-03 3.7799835E-02 at 120iterations finished qdiffx linear iterations at : 23:55:37 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.0816276E-03 3.7799835E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.080000 DelPhi exited at 23:55:37 8.082u 0.866s 0:09.28 96.3% 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 23:55:37 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 = 2444 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: 2.879637 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): -12.74300 40.71000 ymin,ymax (A): -30.41900 25.21300 zmin,zma (A): -9.639000 33.90500 x,y,z range (A): 53.45300 55.63200 43.54400 scale (grids/A): 2.879637 object centre (A): 13.98350 -2.603000 12.13300 number of atom coordinates read : 2444 total number of charged atoms : 2309 net assigned charge : 11.50002 assigned positive charge : 355.3571 centred at (gu) : 88.64658 94.81824 91.37680 assigned negative charge : -343.8579 centred at (gu) : 88.51350 94.86980 91.10000 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169277 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23283 grid for indexing accessible points = 1.400000 m= 83202 mr = 120083 m= 30422 mr = 66725 m= 7489 mr = 23849 m= 1122 mr = 5449 m= 76 mr = 717 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 9039 time to turn everything in is 0.9200000 number of dielectric boundary points 74723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 18471 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) : 1.919758 object centre at (A) : 13.98350 -2.603000 12.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7291326E-02 0.2157178 midg,1,midg; midg,igrid,midg 0.5932497 0.3925938 1,midg,midg; igrid,midg,midg 0.4930277 0.5246149 gauss-seidel spectral radius is 0.9992700 estimated iterations to convergence 292 setup time was (sec) 1.150000 now iterating at: 23:55:38 rms-change max change #iterations 9.579160 399.4570 at 10iterations 5.655816 127.3048 at 20iterations 3.311776 81.89008 at 30iterations 1.929070 41.64372 at 40iterations 1.127034 23.57772 at 50iterations 0.6564856 15.79327 at 60iterations 0.3808952 7.303970 at 70iterations 0.2207856 4.211094 at 80iterations 0.1278065 2.444653 at 90iterations 7.4169844E-02 1.483215 at 100iterations 4.2945217E-02 0.8376541 at 110iterations 2.4845406E-02 0.4589653 at 120iterations 1.4386022E-02 0.2782059 at 130iterations 8.3383741E-03 0.1656129 at 140iterations 4.8236167E-03 9.8471165E-02 at 150iterations 2.8086042E-03 5.8661222E-02 at 160iterations 1.6476476E-03 3.0780792E-02 at 170iterations 9.7867113E-04 1.9999027E-02 at 180iterations finished qdiffx linear iterations at : 23:55:50 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 9.7867113E-04 1.9999027E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 23:55:50 12.423u 0.222s 0:12.97 97.4% 0+0k 0+0io 0pf+0w