Sun Oct 9 16:39:57 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 Sun Oct 9 2011 at 16:39:57 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2832 !!! WARNING: ASL 39 has a net charge of -0.1000 !!! WARNING: GLM 45 has a net charge of -0.0940 !!! WARNING: GLM 114 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6081001 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): 59.02200 116.8300 ymin,ymax (A): -27.05300 22.88800 zmin,zma (A): -18.16300 40.38000 x,y,z range (A): 57.80800 49.94100 58.54300 scale (grids/A): 0.6081001 object centre (A): 87.92600 -2.082500 11.10850 number of atom coordinates read : 2832 total number of charged atoms : 2692 net assigned charge : 0.2120059 assigned positive charge : 416.6914 centred at (gu) : 88.89721 89.80373 92.77087 assigned negative charge : -416.4806 centred at (gu) : 89.03334 89.86813 92.76353 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7094 nv = 96 ne = 84 npr = 55874 no. pairs analyzed = 55874 no. exposed pairs = 3832 no. arc points = 28032 no. surface atoms = 1296 nbur = 1536 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 366 mr = 3502 m= 5 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2200000 number of dielectric boundary points 3927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2787 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8778 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8300046E-10 7.2438711E-10 midg,1,midg; midg,igrid,midg 3.3407737E-09 -3.0607543E-09 1,midg,midg; igrid,midg,midg 8.5993852E-09 -5.3279661E-09 gauss-seidel spectral radius is 0.9860345 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 16:39:58 rms-change max change #iterations 0.1167878 20.80103 at 10iterations 1.0607458E-02 1.642853 at 20iterations 1.1645530E-03 0.2001104 at 30iterations 2.8096361E-04 4.1473389E-02 at 40iterations 1.0107451E-04 1.3720512E-02 at 50iterations finished qdiffx linear iterations at : 16:40:01 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.0107451E-04 1.3720512E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 16:40:02 3.746u 0.203s 0:04.29 91.8% 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 Sun Oct 9 2011 at 16:40:02 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2832 !!! WARNING: ASL 39 has a net charge of -0.1000 !!! WARNING: GLM 45 has a net charge of -0.0940 !!! WARNING: GLM 114 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.824300 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): 59.02200 116.8300 ymin,ymax (A): -27.05300 22.88800 zmin,zma (A): -18.16300 40.38000 x,y,z range (A): 57.80800 49.94100 58.54300 scale (grids/A): 1.824300 object centre (A): 87.92600 -2.082500 11.10850 number of atom coordinates read : 2832 total number of charged atoms : 2692 net assigned charge : 0.2120059 assigned positive charge : 416.6914 centred at (gu) : 86.69102 89.41048 98.31200 assigned negative charge : -416.4806 centred at (gu) : 87.09996 89.60426 98.29034 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76187 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28032 grid for indexing accessible points = 1.400000 m= 25004 mr = 49466 m= 3659 mr = 17288 m= 201 mr = 2083 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 0.3800000 number of dielectric boundary points 36141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 21033 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) : 0.6081001 object centre at (A) : 87.92600 -2.082500 11.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1150308E-03 -9.4358884E-03 midg,1,midg; midg,igrid,midg 3.0561020E-03 -1.5313596E-02 1,midg,midg; igrid,midg,midg 3.9012350E-02 -1.2944548E-02 gauss-seidel spectral radius is 0.9985561 estimated iterations to convergence 209 setup time was (sec) 0.5900000 now iterating at: 16:40:02 rms-change max change #iterations 4.098374 200.7887 at 10iterations 1.859420 71.42097 at 20iterations 0.8496892 29.55612 at 30iterations 0.3893341 12.70924 at 40iterations 0.1784061 6.208544 at 50iterations 8.1628449E-02 2.625731 at 60iterations 3.7331551E-02 1.307869 at 70iterations 1.7076721E-02 0.5428424 at 80iterations 7.9101920E-03 0.2445412 at 90iterations 3.6644058E-03 0.1267776 at 100iterations 1.7193743E-03 5.7554245E-02 at 110iterations 8.3822716E-04 2.8490305E-02 at 120iterations finished qdiffx linear iterations at : 16:40:10 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 8.3822716E-04 2.8490305E-02 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 16:40:11 8.558u 0.239s 0:09.14 96.0% 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 Sun Oct 9 2011 at 16:40:11 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2832 !!! WARNING: ASL 39 has a net charge of -0.1000 !!! WARNING: GLM 45 has a net charge of -0.0940 !!! WARNING: GLM 114 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.736450 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): 59.02200 116.8300 ymin,ymax (A): -27.05300 22.88800 zmin,zma (A): -18.16300 40.38000 x,y,z range (A): 57.80800 49.94100 58.54300 scale (grids/A): 2.736450 object centre (A): 87.92600 -2.082500 11.10850 number of atom coordinates read : 2832 total number of charged atoms : 2692 net assigned charge : 0.2120059 assigned positive charge : 416.6914 centred at (gu) : 85.03632 89.11556 102.4679 assigned negative charge : -416.4806 centred at (gu) : 85.64986 89.40642 102.4354 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 176412 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28032 grid for indexing accessible points = 1.400000 m= 81753 mr = 121197 m= 27868 mr = 64179 m= 6328 mr = 21275 m= 826 mr = 4533 m= 46 mr = 549 m= 0 mr = 10 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2592 time to turn everything in is 0.9600000 number of dielectric boundary points 81490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 21530 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) : 1.824300 object centre at (A) : 87.92600 -2.082500 11.10850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1964555 -0.2311680 midg,1,midg; midg,igrid,midg 6.7863785E-02 -0.2700782 1,midg,midg; igrid,midg,midg 0.8278812 -0.1810401 gauss-seidel spectral radius is 0.9992610 estimated iterations to convergence 290 setup time was (sec) 1.190000 now iterating at: 16:40:12 rms-change max change #iterations 9.852801 410.0089 at 10iterations 5.834992 161.1336 at 20iterations 3.422740 78.28751 at 30iterations 1.999763 42.21844 at 40iterations 1.160453 27.09488 at 50iterations 0.6734645 13.73593 at 60iterations 0.3902090 7.165289 at 70iterations 0.2252180 4.832382 at 80iterations 0.1304355 2.367750 at 90iterations 7.5185783E-02 1.392233 at 100iterations 4.3309260E-02 0.8161457 at 110iterations 2.4919875E-02 0.4823256 at 120iterations 1.4377581E-02 0.2660193 at 130iterations 8.2822302E-03 0.1624498 at 140iterations 4.8030266E-03 8.8441849E-02 at 150iterations 2.7890436E-03 5.4496765E-02 at 160iterations 1.6381296E-03 3.1739831E-02 at 170iterations 9.8157453E-04 1.9543648E-02 at 180iterations finished qdiffx linear iterations at : 16:40:25 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 9.8157453E-04 1.9543648E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 16:40:25 12.870u 1.105s 0:14.38 97.1% 0+0k 0+0io 0pf+0w