Tue Oct 11 06:00:20 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 06:00:20 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! 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: 0.7095875 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): 3.499000 47.23200 ymin,ymax (A): 0.8530000 40.01800 zmin,zma (A): -3.816000 46.35400 x,y,z range (A): 43.73300 39.16500 50.17000 scale (grids/A): 0.7095875 object centre (A): 25.36550 20.43550 21.26900 number of atom coordinates read : 2040 total number of charged atoms : 1902 net assigned charge : 6.837009 assigned positive charge : 309.1791 centred at (gu) : 89.92976 90.82616 89.86901 assigned negative charge : -302.3421 centred at (gu) : 90.10715 90.80108 89.88709 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7055 nv = 96 ne = 84 npr = 40888 no. pairs analyzed = 40888 no. exposed pairs = 2463 no. arc points = 16862 no. surface atoms = 836 nbur = 1204 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 474 mr = 4085 m= 5 mr = 79 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 0.1800000 number of dielectric boundary points 3370 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1598 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7714 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.1361683E-08 5.0212378E-08 midg,1,midg; midg,igrid,midg 4.1176570E-08 8.5572680E-08 1,midg,midg; igrid,midg,midg 1.5017648E-07 -2.9727483E-08 gauss-seidel spectral radius is 0.9896431 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:00:21 rms-change max change #iterations 0.2053744 31.56574 at 10iterations 2.5847029E-02 3.301121 at 20iterations 3.6028358E-03 0.5015411 at 30iterations 6.5492134E-04 8.0715179E-02 at 40iterations 1.6896252E-04 2.1537781E-02 at 50iterations finished qdiffx linear iterations at : 06:00:24 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.6896252E-04 2.1537781E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:00:24 3.368u 0.172s 0:04.21 83.8% 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 Tue Oct 11 2011 at 06:00:24 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! 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: 2.128762 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): 3.499000 47.23200 ymin,ymax (A): 0.8530000 40.01800 zmin,zma (A): -3.816000 46.35400 x,y,z range (A): 43.73300 39.16500 50.17000 scale (grids/A): 2.128762 object centre (A): 25.36550 20.43550 21.26900 number of atom coordinates read : 2040 total number of charged atoms : 1902 net assigned charge : 6.837009 assigned positive charge : 309.1791 centred at (gu) : 89.78912 92.47831 89.60727 assigned negative charge : -302.3421 centred at (gu) : 90.32157 92.40328 89.66151 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74789 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 30727 mr = 53393 m= 6201 mr = 23541 m= 550 mr = 4173 m= 13 mr = 265 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 30905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 15105 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) : 0.7095875 object centre at (A) : 25.36550 20.43550 21.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3640061E-02 5.4401394E-02 midg,1,midg; midg,igrid,midg 4.5435466E-03 3.0561134E-02 1,midg,midg; igrid,midg,midg 4.9552895E-02 1.1838240E-02 gauss-seidel spectral radius is 0.9988325 estimated iterations to convergence 232 setup time was (sec) 0.5900000 now iterating at: 06:00:25 rms-change max change #iterations 4.578847 236.5525 at 10iterations 2.271389 74.58014 at 20iterations 1.127002 38.55527 at 30iterations 0.5609092 21.36645 at 40iterations 0.2784522 9.016510 at 50iterations 0.1387662 4.883883 at 60iterations 6.9292292E-02 2.273632 at 70iterations 3.4535963E-02 1.074833 at 80iterations 1.7294468E-02 0.5723076 at 90iterations 8.6987810E-03 0.2731209 at 100iterations 4.4165556E-03 0.1337504 at 110iterations 2.2948391E-03 6.8099976E-02 at 120iterations finished qdiffx linear iterations at : 06:00:32 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.2948391E-03 6.8099976E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 06:00:33 7.830u 0.187s 0:08.29 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 Tue Oct 11 2011 at 06:00:34 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2040 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! 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: 3.193143 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): 3.499000 47.23200 ymin,ymax (A): 0.8530000 40.01800 zmin,zma (A): -3.816000 46.35400 x,y,z range (A): 43.73300 39.16500 50.17000 scale (grids/A): 3.193143 object centre (A): 25.36550 20.43550 21.26900 number of atom coordinates read : 2040 total number of charged atoms : 1902 net assigned charge : 6.837009 assigned positive charge : 309.1791 centred at (gu) : 89.68373 93.71749 89.41085 assigned negative charge : -302.3421 centred at (gu) : 90.48239 93.60487 89.49223 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 172162 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 94961 mr = 128380 m= 39642 mr = 79414 m= 11799 mr = 32694 m= 2317 mr = 9209 m= 235 mr = 1675 m= 8 mr = 140 m= 0 mr = 4 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 69608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15216 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) : 2.128762 object centre at (A) : 25.36550 20.43550 21.26900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1452690 0.5480486 midg,1,midg; midg,igrid,midg 1.6307170E-02 0.2229243 1,midg,midg; igrid,midg,midg 0.3896914 0.2140981 gauss-seidel spectral radius is 0.9992930 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 06:00:35 rms-change max change #iterations 10.20469 295.8572 at 10iterations 6.041499 153.7764 at 20iterations 3.572254 72.14272 at 30iterations 2.108954 40.93715 at 40iterations 1.239872 25.45849 at 50iterations 0.7280490 17.62999 at 60iterations 0.4275107 8.022668 at 70iterations 0.2511514 4.763797 at 80iterations 0.1468807 2.535091 at 90iterations 8.6303033E-02 1.755499 at 100iterations 5.0729785E-02 0.9395609 at 110iterations 2.9957514E-02 0.6224289 at 120iterations 1.7904866E-02 0.3345833 at 130iterations 1.0891037E-02 0.2074575 at 140iterations 6.8224012E-03 0.1291742 at 150iterations 4.4549904E-03 9.6084595E-02 at 160iterations 3.0834838E-03 5.7975769E-02 at 170iterations 2.2592049E-03 4.2407990E-02 at 180iterations finished qdiffx linear iterations at : 06:00:47 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 2.2592049E-03 4.2407990E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 06:00:47 12.821u 0.204s 0:13.40 97.1% 0+0k 0+0io 0pf+0w