Tue Oct 11 08:20:36 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 Tue Oct 11 2011 at 08:20:36 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2757 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6351245 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): -5.265000 50.78700 ymin,ymax (A): -16.09400 29.59900 zmin,zma (A): 57.61900 109.4130 x,y,z range (A): 56.05200 45.69300 51.79400 scale (grids/A): 0.6351245 object centre (A): 22.76100 6.752501 83.51600 number of atom coordinates read : 2757 total number of charged atoms : 2605 net assigned charge : 5.312018 assigned positive charge : 417.4776 centred at (gu) : 90.05779 90.16505 89.50494 assigned negative charge : -412.1662 centred at (gu) : 90.30731 90.08658 89.55194 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7420 nv = 96 ne = 84 npr = 55859 no. pairs analyzed = 55859 no. exposed pairs = 3226 no. arc points = 22709 no. surface atoms = 1093 nbur = 1664 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 4249 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.3200000 number of dielectric boundary points 3507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2186 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8912 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3118774E-08 1.4812382E-09 midg,1,midg; midg,igrid,midg -1.7688703E-09 1.5713844E-08 1,midg,midg; igrid,midg,midg 3.2642518E-08 -2.1347752E-08 gauss-seidel spectral radius is 0.9871684 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 08:20:37 rms-change max change #iterations 0.1514298 24.74420 at 10iterations 1.5077588E-02 2.318167 at 20iterations 2.0936236E-03 0.3687019 at 30iterations 5.3417945E-04 0.1151505 at 40iterations 1.6590177E-04 3.6781311E-02 at 50iterations finished qdiffx linear iterations at : 08:20:42 total time elapsed so far: 5.300000 # loops : 50 mean,max change (kT/e) : 1.6590177E-04 3.6781311E-02 energy calculations done at 5.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.480000 DelPhi exited at 08:20:43 5.480u 0.770s 0:06.82 91.6% 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 08:20:43 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2757 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.905374 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): -5.265000 50.78700 ymin,ymax (A): -16.09400 29.59900 zmin,zma (A): 57.61900 109.4130 x,y,z range (A): 56.05200 45.69300 51.79400 scale (grids/A): 1.905374 object centre (A): 22.76100 6.752501 83.51600 number of atom coordinates read : 2757 total number of charged atoms : 2605 net assigned charge : 5.312018 assigned positive charge : 417.4776 centred at (gu) : 90.17280 90.49456 88.51390 assigned negative charge : -412.1662 centred at (gu) : 90.92191 90.25945 88.65546 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22709 grid for indexing accessible points = 1.400000 m= 29096 mr = 57000 m= 4387 mr = 21854 m= 259 mr = 2868 m= 2 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 3710 time to turn everything in is 0.6500000 number of dielectric boundary points 32491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 20481 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) : 0.6351245 object centre at (A) : 22.76100 6.752501 83.51600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9543016E-03 7.1503236E-03 midg,1,midg; midg,igrid,midg 1.3322525E-02 2.1145599E-02 1,midg,midg; igrid,midg,midg 4.7559422E-02 -4.0061358E-02 gauss-seidel spectral radius is 0.9986480 estimated iterations to convergence 216 setup time was (sec) 0.9400000 now iterating at: 08:20:44 rms-change max change #iterations 4.437750 174.1965 at 10iterations 2.078895 69.39288 at 20iterations 0.9771505 29.50825 at 30iterations 0.4587811 15.89703 at 40iterations 0.2156963 6.462632 at 50iterations 0.1016273 3.440692 at 60iterations 4.7982693E-02 1.404636 at 70iterations 2.2713248E-02 0.7272816 at 80iterations 1.0806015E-02 0.3573227 at 90iterations 5.2055423E-03 0.1691475 at 100iterations 2.5733204E-03 9.8060608E-02 at 110iterations 1.3316349E-03 4.8061371E-02 at 120iterations finished qdiffx linear iterations at : 08:20:55 total time elapsed so far: 11.34000 # loops : 120 mean,max change (kT/e) : 1.3316349E-03 4.8061371E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.51000 DelPhi exited at 08:20:56 11.512u 0.492s 0:12.48 96.1% 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 08:20:56 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2757 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.858060 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): -5.265000 50.78700 ymin,ymax (A): -16.09400 29.59900 zmin,zma (A): 57.61900 109.4130 x,y,z range (A): 56.05200 45.69300 51.79400 scale (grids/A): 2.858060 object centre (A): 22.76100 6.752501 83.51600 number of atom coordinates read : 2757 total number of charged atoms : 2605 net assigned charge : 5.312018 assigned positive charge : 417.4776 centred at (gu) : 90.25893 90.74164 87.77086 assigned negative charge : -412.1662 centred at (gu) : 91.38277 90.38909 87.98309 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 186649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22709 grid for indexing accessible points = 1.400000 m= 94642 mr = 137832 m= 33660 mr = 78536 m= 8033 mr = 27445 m= 1179 mr = 6269 m= 64 mr = 854 m= 0 mr = 14 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 12193 time to turn everything in is 1.710000 number of dielectric boundary points 73277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 20836 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) : 1.905374 object centre at (A) : 22.76100 6.752501 83.51600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3781677E-02 1.6326319E-02 midg,1,midg; midg,igrid,midg 0.2008907 0.2210002 1,midg,midg; igrid,midg,midg 0.5610960 -0.2652311 gauss-seidel spectral radius is 0.9992575 estimated iterations to convergence 290 setup time was (sec) 2.030000 now iterating at: 08:20:58 rms-change max change #iterations 10.25182 337.5099 at 10iterations 5.952816 147.7573 at 20iterations 3.445722 68.23411 at 30iterations 1.988099 35.47533 at 40iterations 1.143871 25.09207 at 50iterations 0.6606184 12.58805 at 60iterations 0.3790801 6.981297 at 70iterations 0.2178715 4.104401 at 80iterations 0.1251400 2.131325 at 90iterations 7.1858101E-02 1.393322 at 100iterations 4.1438803E-02 0.7141094 at 110iterations 2.3864644E-02 0.4109573 at 120iterations 1.3765668E-02 0.2789459 at 130iterations 7.9895025E-03 0.1454811 at 140iterations 4.6969890E-03 9.4429016E-02 at 150iterations 2.8052940E-03 5.4718018E-02 at 160iterations 1.7315979E-03 4.3888092E-02 at 170iterations 1.1255073E-03 2.6420593E-02 at 180iterations finished qdiffx linear iterations at : 08:21:16 total time elapsed so far: 19.71000 # loops : 180 mean,max change (kT/e) : 1.1255073E-03 2.6420593E-02 energy calculations done at 19.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.89000 DelPhi exited at 08:21:17 19.891u 0.560s 0:21.23 96.3% 0+0k 0+0io 0pf+0w