Tue Oct 11 01:13:39 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 01:13:39 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 = 2623 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5925334 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): -34.14900 19.69500 ymin,ymax (A): 15.45300 75.53400 zmin,zma (A): 16.90200 60.10100 x,y,z range (A): 53.84400 60.08100 43.19900 scale (grids/A): 0.5925334 object centre (A): -7.227001 45.49350 38.50150 number of atom coordinates read : 2623 total number of charged atoms : 2477 net assigned charge : 3.406015 assigned positive charge : 394.7479 centred at (gu) : 89.22893 90.30419 90.27019 assigned negative charge : -391.3424 centred at (gu) : 89.22071 90.58286 90.09252 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6040 nv = 96 ne = 84 npr = 53327 no. pairs analyzed = 53327 no. exposed pairs = 3079 no. arc points = 21741 no. surface atoms = 1047 nbur = 1576 mkacc time = 0.1300000 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 = 1.456000 m= 258 mr = 3356 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3100000 number of dielectric boundary points 2921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2173 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8520613E-09 6.6398811E-09 midg,1,midg; midg,igrid,midg 8.4093266E-09 -7.7458484E-09 1,midg,midg; igrid,midg,midg 1.1058098E-09 1.1878600E-09 gauss-seidel spectral radius is 0.9852607 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 01:13:40 rms-change max change #iterations 0.1043468 20.64311 at 10iterations 9.2242435E-03 1.351181 at 20iterations 1.1444730E-03 0.2484741 at 30iterations 2.6660840E-04 6.6642761E-02 at 40iterations 7.1027585E-05 1.8360138E-02 at 50iterations finished qdiffx linear iterations at : 01:13:45 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 7.1027585E-05 1.8360138E-02 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.880000 DelPhi exited at 01:13:45 4.887u 0.404s 0:05.79 91.1% 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 01:13:45 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 = 2623 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.777600 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): -34.14900 19.69500 ymin,ymax (A): 15.45300 75.53400 zmin,zma (A): 16.90200 60.10100 x,y,z range (A): 53.84400 60.08100 43.19900 scale (grids/A): 1.777600 object centre (A): -7.227001 45.49350 38.50150 number of atom coordinates read : 2623 total number of charged atoms : 2477 net assigned charge : 3.406015 assigned positive charge : 394.7479 centred at (gu) : 87.68598 90.91212 90.80995 assigned negative charge : -391.3424 centred at (gu) : 87.66196 91.74836 90.27732 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 66782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21741 grid for indexing accessible points = 1.400000 m= 21949 mr = 46963 m= 2771 mr = 16051 m= 90 mr = 1639 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1264 time to turn everything in is 0.5300000 number of dielectric boundary points 26921 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 191 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19318 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) : 0.5925334 object centre at (A) : -7.227001 45.49350 38.50150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4319752E-03 2.5612930E-02 midg,1,midg; midg,igrid,midg -1.0314626E-02 -6.6297442E-02 1,midg,midg; igrid,midg,midg -2.6322476E-04 6.7935120E-03 gauss-seidel spectral radius is 0.9984346 estimated iterations to convergence 201 setup time was (sec) 0.8100000 now iterating at: 01:13:47 rms-change max change #iterations 3.679216 166.3788 at 10iterations 1.628429 70.81012 at 20iterations 0.7234259 29.05711 at 30iterations 0.3211710 11.91038 at 40iterations 0.1431271 4.654305 at 50iterations 6.3778721E-02 2.171097 at 60iterations 2.8221151E-02 0.9581223 at 70iterations 1.2678294E-02 0.4363785 at 80iterations 5.7032481E-03 0.1978302 at 90iterations 2.6079402E-03 9.6179962E-02 at 100iterations 1.2375599E-03 4.5574188E-02 at 110iterations 6.1112177E-04 2.4738312E-02 at 120iterations finished qdiffx linear iterations at : 01:13:56 total time elapsed so far: 10.72000 # loops : 120 mean,max change (kT/e) : 6.1112177E-04 2.4738312E-02 energy calculations done at 10.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 01:13:57 10.886u 0.478s 0:11.95 94.9% 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 01:13:57 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2623 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.666400 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): -34.14900 19.69500 ymin,ymax (A): 15.45300 75.53400 zmin,zma (A): 16.90200 60.10100 x,y,z range (A): 53.84400 60.08100 43.19900 scale (grids/A): 2.666400 object centre (A): -7.227001 45.49350 38.50150 number of atom coordinates read : 2623 total number of charged atoms : 2477 net assigned charge : 3.406015 assigned positive charge : 394.7479 centred at (gu) : 86.52882 91.36795 91.21478 assigned negative charge : -391.3424 centred at (gu) : 86.49282 92.62244 90.41587 start vw surface at 0.1300000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 155247 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21741 grid for indexing accessible points = 1.400000 m= 74361 mr = 114468 m= 23394 mr = 60839 m= 4820 mr = 18513 m= 421 mr = 3593 m= 8 mr = 245 m= 0 mr = 2 time to grow re-entrant surface = 0.8000001 no. cavity mid-points inaccessible to solvent = 4140 time to turn everything in is 1.370000 number of dielectric boundary points 60591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 19806 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) : 1.777600 object centre at (A) : -7.227001 45.49350 38.50150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2414976E-02 0.2937419 midg,1,midg; midg,igrid,midg -0.5963939 -0.9150996 1,midg,midg; igrid,midg,midg -2.0166384E-02 5.5907339E-02 gauss-seidel spectral radius is 0.9991972 estimated iterations to convergence 279 setup time was (sec) 1.760000 now iterating at: 01:13:59 rms-change max change #iterations 8.913305 309.3328 at 10iterations 5.052537 124.0724 at 20iterations 2.847508 54.69617 at 30iterations 1.605003 36.41195 at 40iterations 0.9000499 17.73475 at 50iterations 0.5070420 11.03835 at 60iterations 0.2848762 6.009769 at 70iterations 0.1597334 3.197693 at 80iterations 8.9675486E-02 1.991320 at 90iterations 5.0305918E-02 0.9545059 at 100iterations 2.8273765E-02 0.5379562 at 110iterations 1.5859656E-02 0.3177065 at 120iterations 8.9481240E-03 0.1701851 at 130iterations 5.0285016E-03 0.1003089 at 140iterations 2.8502846E-03 5.5212021E-02 at 150iterations 1.6295920E-03 3.8120270E-02 at 160iterations 9.4790675E-04 2.0942688E-02 at 170iterations 5.6640821E-04 1.2451172E-02 at 180iterations finished qdiffx linear iterations at : 01:14:16 total time elapsed so far: 17.84000 # loops : 180 mean,max change (kT/e) : 5.6640821E-04 1.2451172E-02 energy calculations done at 17.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.00000 DelPhi exited at 01:14:16 18.005u 0.455s 0:19.14 96.3% 0+0k 0+0io 0pf+0w