Mon Oct 10 11:06:59 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+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 Mon Oct 10 2011 at 11:06:59 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: HIR 717 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5011191 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): 43.56300 114.6040 ymin,ymax (A): -25.27600 39.64000 zmin,zma (A): -32.78500 33.83900 x,y,z range (A): 71.04100 64.91600 66.62399 scale (grids/A): 0.5011191 object centre (A): 79.08350 7.182002 0.5269985 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 7.514055 assigned positive charge : 847.2799 centred at (gu) : 90.55849 89.39186 91.04021 assigned negative charge : -839.7739 centred at (gu) : 90.52748 89.41007 91.05011 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8533 nv = 96 ne = 84 npr = 105469 no. pairs analyzed = 105469 no. exposed pairs = 6422 no. arc points = 43610 no. surface atoms = 2155 nbur = 3194 mkacc time = 0.2700000 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 = 1.736000 m= 286 mr = 4670 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4290 ## 657 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 11465 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7534089E-11 6.3717753E-11 midg,1,midg; midg,igrid,midg 1.2381043E-10 2.7493240E-11 1,midg,midg; igrid,midg,midg 5.5097480E-12 1.5203863E-10 gauss-seidel spectral radius is 0.9796751 estimated iterations to convergence 58 setup time was (sec) 0.7800000 now iterating at: 11:07:00 rms-change max change #iterations 6.6497065E-02 9.674807 at 10iterations 3.5393140E-03 0.4592857 at 20iterations 3.5337434E-04 5.5303574E-02 at 30iterations 1.4638714E-04 2.3899376E-02 at 40iterations 7.4672724E-05 1.2074649E-02 at 50iterations finished qdiffx linear iterations at : 11:07:02 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 7.4672724E-05 1.2074649E-02 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 11:07:03 3.546u 0.240s 0:04.16 90.8% 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 Mon Oct 10 2011 at 11:07:13 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: HIR 717 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.503357 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): 43.56300 114.6040 ymin,ymax (A): -25.27600 39.64000 zmin,zma (A): -32.78500 33.83900 x,y,z range (A): 71.04100 64.91600 66.62399 scale (grids/A): 1.503357 object centre (A): 79.08350 7.182002 0.5269985 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 7.514055 assigned positive charge : 847.2799 centred at (gu) : 91.67397 88.17434 93.11911 assigned negative charge : -839.7739 centred at (gu) : 91.58263 88.23035 93.15021 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 98972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43610 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 28408 mr = 70506 m= 2261 mr = 19346 m= 29 mr = 965 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1870 time to turn everything in is 0.6500000 number of dielectric boundary points 38853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 607 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 38625 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) : 0.5011191 object centre at (A) : 79.08350 7.182002 0.5269985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5037232E-03 -3.6538662E-03 midg,1,midg; midg,igrid,midg 1.2282162E-02 -1.6387625E-03 1,midg,midg; igrid,midg,midg -2.3569593E-02 9.0219378E-03 gauss-seidel spectral radius is 0.9980733 estimated iterations to convergence 181 setup time was (sec) 0.9500000 now iterating at: 11:07:15 rms-change max change #iterations 3.970314 149.3614 at 10iterations 1.610099 54.11904 at 20iterations 0.6553449 20.42552 at 30iterations 0.2667248 8.731615 at 40iterations 0.1086774 3.371380 at 50iterations 4.4210088E-02 1.355238 at 60iterations 1.8002568E-02 0.5221739 at 70iterations 7.3685423E-03 0.2737255 at 80iterations 3.0111033E-03 8.6743355E-02 at 90iterations 1.2656843E-03 4.2354584E-02 at 100iterations 5.6686986E-04 1.8848419E-02 at 110iterations 2.9610508E-04 1.0661602E-02 at 120iterations finished qdiffx linear iterations at : 11:07:21 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.9610508E-04 1.0661602E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 11:07:22 7.710u 0.243s 0:08.25 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 Mon Oct 10 2011 at 11:07:22 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5349 !!! WARNING: HIR 717 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.255036 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): 43.56300 114.6040 ymin,ymax (A): -25.27600 39.64000 zmin,zma (A): -32.78500 33.83900 x,y,z range (A): 71.04100 64.91600 66.62399 scale (grids/A): 2.255036 object centre (A): 79.08350 7.182002 0.5269985 number of atom coordinates read : 5349 total number of charged atoms : 5193 net assigned charge : 7.514055 assigned positive charge : 847.2799 centred at (gu) : 92.51021 87.26102 94.67822 assigned negative charge : -839.7739 centred at (gu) : 92.37390 87.34550 94.72511 start vw surface at 0.1900000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 231136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43610 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 104240 mr = 172805 m= 24888 mr = 82905 m= 3109 mr = 18174 m= 144 mr = 1918 m= 1 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 6303 time to turn everything in is 1.600000 number of dielectric boundary points 87665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 41391 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) : 1.503357 object centre at (A) : 79.08350 7.182002 0.5269985 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1308819E-02 -0.2181452 midg,1,midg; midg,igrid,midg 0.3189912 -6.0403362E-02 1,midg,midg; igrid,midg,midg -0.7669057 0.1532185 gauss-seidel spectral radius is 0.9991523 estimated iterations to convergence 271 setup time was (sec) 1.920000 now iterating at: 11:07:24 rms-change max change #iterations 10.87408 284.0682 at 10iterations 6.208116 160.3126 at 20iterations 3.516326 77.29940 at 30iterations 1.979308 40.85139 at 40iterations 1.107382 21.44055 at 50iterations 0.6188003 12.68775 at 60iterations 0.3445046 6.488110 at 70iterations 0.1917623 3.479692 at 80iterations 0.1065987 1.914921 at 90iterations 5.9173074E-02 1.031494 at 100iterations 3.2839142E-02 0.5706594 at 110iterations 1.8206477E-02 0.3846025 at 120iterations 1.0077378E-02 0.1919785 at 130iterations 5.5939029E-03 0.1069325 at 140iterations 3.1058763E-03 5.8270454E-02 at 150iterations 1.7268325E-03 3.0601501E-02 at 160iterations 9.6673152E-04 1.9165039E-02 at 170iterations 5.5052666E-04 1.2294769E-02 at 180iterations finished qdiffx linear iterations at : 11:07:34 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 5.5052666E-04 1.2294769E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 11:07:35 12.667u 0.257s 0:13.23 97.5% 0+0k 0+0io 0pf+0w