Sun Oct 9 11:43:54 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+sph.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 = amb.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 11:43:54 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 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: 0.6527079 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): -4.918000 47.53700 ymin,ymax (A): 8.891001 60.25100 zmin,zma (A): 4.648000 59.19000 x,y,z range (A): 52.45500 51.36000 54.54200 scale (grids/A): 0.6527079 object centre (A): 21.30950 34.57100 31.91900 number of atom coordinates read : 2703 total number of charged atoms : 2641 net assigned charge : 3.500010 assigned positive charge : 406.2921 centred at (gu) : 90.73191 90.21551 90.94112 assigned negative charge : -402.7937 centred at (gu) : 90.78696 90.16579 90.93063 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8227 nv = 96 ne = 84 npr = 50366 no. pairs analyzed = 50366 no. exposed pairs = 3802 no. arc points = 27448 no. surface atoms = 1268 nbur = 1435 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 570 mr = 4183 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 9.0000011E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2579 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5960138E-09 1.1048725E-08 midg,1,midg; midg,igrid,midg -1.0976334E-09 1.6443902E-08 1,midg,midg; igrid,midg,midg 1.4264113E-08 -2.5151077E-09 gauss-seidel spectral radius is 0.9878697 estimated iterations to convergence 74 setup time was (sec) 0.4000000 now iterating at: 11:43:55 rms-change max change #iterations 0.1609896 23.23993 at 10iterations 1.6634816E-02 2.154747 at 20iterations 1.7090538E-03 0.2340641 at 30iterations 1.8773288E-04 2.6332855E-02 at 40iterations 3.1059892E-05 5.8879852E-03 at 50iterations finished qdiffx linear iterations at : 11:43:58 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.1059892E-05 5.8879852E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 11:43:58 3.386u 0.166s 0:03.84 92.1% 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 Sun Oct 9 2011 at 11:43:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 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: 1.958124 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): -4.918000 47.53700 ymin,ymax (A): 8.891001 60.25100 zmin,zma (A): 4.648000 59.19000 x,y,z range (A): 52.45500 51.36000 54.54200 scale (grids/A): 1.958124 object centre (A): 21.30950 34.57100 31.91900 number of atom coordinates read : 2703 total number of charged atoms : 2641 net assigned charge : 3.500010 assigned positive charge : 406.2921 centred at (gu) : 92.19465 90.64584 92.82227 assigned negative charge : -402.7937 centred at (gu) : 92.36089 90.49724 92.79172 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27448 grid for indexing accessible points = 1.400000 m= 33290 mr = 58164 m= 6594 mr = 23744 m= 524 mr = 4253 m= 11 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 366 time to turn everything in is 0.4300000 number of dielectric boundary points 42038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20862 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) : 0.6527079 object centre at (A) : 21.30950 34.57100 31.91900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9905130E-03 3.1910442E-02 midg,1,midg; midg,igrid,midg -4.1831224E-03 3.0436017E-02 1,midg,midg; igrid,midg,midg 3.4557292E-04 -9.0012448E-03 gauss-seidel spectral radius is 0.9987525 estimated iterations to convergence 224 setup time was (sec) 0.6500000 now iterating at: 11:43:59 rms-change max change #iterations 4.585981 197.4286 at 10iterations 2.215708 82.18589 at 20iterations 1.068934 36.59193 at 30iterations 0.5179008 15.65159 at 40iterations 0.2506333 7.921928 at 50iterations 0.1207430 3.761013 at 60iterations 5.8346827E-02 1.643165 at 70iterations 2.8238231E-02 0.8174171 at 80iterations 1.3631203E-02 0.4016552 at 90iterations 6.6003036E-03 0.1946774 at 100iterations 3.1959219E-03 9.5445633E-02 at 110iterations 1.5467256E-03 4.3884277E-02 at 120iterations finished qdiffx linear iterations at : 11:44:06 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.5467256E-03 4.3884277E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 11:44:07 7.905u 0.199s 0:08.38 96.5% 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 11:44:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2703 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: 2.937186 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): -4.918000 47.53700 ymin,ymax (A): 8.891001 60.25100 zmin,zma (A): 4.648000 59.19000 x,y,z range (A): 52.45500 51.36000 54.54200 scale (grids/A): 2.937186 object centre (A): 21.30950 34.57100 31.91900 number of atom coordinates read : 2703 total number of charged atoms : 2641 net assigned charge : 3.500010 assigned positive charge : 406.2921 centred at (gu) : 93.29189 90.96857 94.23318 assigned negative charge : -402.7937 centred at (gu) : 93.54128 90.74585 94.18743 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 202809 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27448 grid for indexing accessible points = 1.400000 m= 102791 mr = 141753 m= 42060 mr = 81640 m= 12534 mr = 33375 m= 2176 mr = 9432 m= 168 mr = 1478 m= 3 mr = 81 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1162 time to turn everything in is 1.140000 number of dielectric boundary points 94782 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 21128 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) : 1.958124 object centre at (A) : 21.30950 34.57100 31.91900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2519014E-03 0.3899365 midg,1,midg; midg,igrid,midg -7.9309029E-06 0.3435229 1,midg,midg; igrid,midg,midg -5.1107496E-02 -4.4167731E-02 gauss-seidel spectral radius is 0.9993185 estimated iterations to convergence 302 setup time was (sec) 1.370000 now iterating at: 11:44:08 rms-change max change #iterations 10.88063 470.6285 at 10iterations 6.630471 177.9315 at 20iterations 4.018120 92.18257 at 30iterations 2.412584 53.64218 at 40iterations 1.442501 28.17463 at 50iterations 0.8628117 19.12844 at 60iterations 0.5133855 9.920410 at 70iterations 0.3048009 5.337093 at 80iterations 0.1804693 3.526438 at 90iterations 0.1064078 2.054253 at 100iterations 6.2994637E-02 1.143684 at 110iterations 3.7208799E-02 0.6410294 at 120iterations 2.1930175E-02 0.3679008 at 130iterations 1.2937302E-02 0.2213688 at 140iterations 7.6272022E-03 0.1388450 at 150iterations 4.5072990E-03 7.4604988E-02 at 160iterations 2.6663453E-03 5.2246094E-02 at 170iterations 1.5811843E-03 2.5735855E-02 at 180iterations finished qdiffx linear iterations at : 11:44:20 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 1.5811843E-03 2.5735855E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 11:44:20 13.228u 0.220s 0:13.73 97.8% 0+0k 0+0io 0pf+0w