Tue Oct 11 06:23:45 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 06:23:45 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2031 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 0.7181618 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): 3.364000 47.22800 ymin,ymax (A): 0.6669999 42.36000 zmin,zma (A): -2.602000 46.96900 x,y,z range (A): 43.86400 41.69300 49.57100 scale (grids/A): 0.7181618 object centre (A): 25.29600 21.51350 22.18350 number of atom coordinates read : 2031 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.85403 89.91313 90.31443 assigned negative charge : -304.4261 centred at (gu) : 90.04620 89.89642 90.34353 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7167 nv = 96 ne = 84 npr = 40443 no. pairs analyzed = 40443 no. exposed pairs = 2470 no. arc points = 16802 no. surface atoms = 838 nbur = 1193 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4177 m= 6 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3401 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1613 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7908 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7518160E-08 6.0636630E-08 midg,1,midg; midg,igrid,midg 6.5914364E-08 8.3915459E-08 1,midg,midg; igrid,midg,midg 1.9572997E-07 -4.3169280E-08 gauss-seidel spectral radius is 0.9898865 estimated iterations to convergence 81 setup time was (sec) 0.5700000 now iterating at: 06:23:46 rms-change max change #iterations 0.2176364 31.20242 at 10iterations 2.8047271E-02 3.683258 at 20iterations 3.8069936E-03 0.5040283 at 30iterations 6.2738801E-04 8.5060120E-02 at 40iterations 1.4351615E-04 1.7375946E-02 at 50iterations finished qdiffx linear iterations at : 06:23:49 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.4351615E-04 1.7375946E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 06:23:50 4.073u 0.275s 0:04.64 93.5% 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 Tue Oct 11 2011 at 06:23:50 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2031 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 2.154485 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): 3.364000 47.22800 ymin,ymax (A): 0.6669999 42.36000 zmin,zma (A): -2.602000 46.96900 x,y,z range (A): 43.86400 41.69300 49.57100 scale (grids/A): 2.154485 object centre (A): 25.29600 21.51350 22.18350 number of atom coordinates read : 2031 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.56181 89.73969 90.94361 assigned negative charge : -304.4261 centred at (gu) : 90.13849 89.68939 91.03066 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 76038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16802 grid for indexing accessible points = 1.400000 m= 30778 mr = 54238 m= 6103 mr = 23544 m= 593 mr = 4052 m= 13 mr = 296 m= 0 mr = 2 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 31393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15280 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) : 0.7181618 object centre at (A) : 25.29600 21.51350 22.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4605007E-02 6.6479146E-02 midg,1,midg; midg,igrid,midg 5.4583009E-03 2.6344707E-02 1,midg,midg; igrid,midg,midg 5.0837938E-02 7.1486318E-03 gauss-seidel spectral radius is 0.9988568 estimated iterations to convergence 234 setup time was (sec) 1.020000 now iterating at: 06:23:51 rms-change max change #iterations 4.661593 170.9301 at 10iterations 2.318930 76.75080 at 20iterations 1.164782 36.03293 at 30iterations 0.5810018 18.23520 at 40iterations 0.2914202 8.653088 at 50iterations 0.1456626 4.548117 at 60iterations 7.3136695E-02 2.593880 at 70iterations 3.6568791E-02 1.052525 at 80iterations 1.8360026E-02 0.5867729 at 90iterations 9.3120635E-03 0.2752190 at 100iterations 4.7438191E-03 0.1466322 at 110iterations 2.4485395E-03 7.2734833E-02 at 120iterations finished qdiffx linear iterations at : 06:24:00 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 2.4485395E-03 7.2734833E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 06:24:00 9.658u 0.297s 0:10.42 95.3% 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 Tue Oct 11 2011 at 06:24:00 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2031 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 3.231728 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): 3.364000 47.22800 ymin,ymax (A): 0.6669999 42.36000 zmin,zma (A): -2.602000 46.96900 x,y,z range (A): 43.86400 41.69300 49.57100 scale (grids/A): 3.231728 object centre (A): 25.29600 21.51350 22.18350 number of atom coordinates read : 2031 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 89.34280 89.60951 91.41538 assigned negative charge : -304.4261 centred at (gu) : 90.20763 89.53415 91.54604 start vw surface at 0.1500000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 175462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16802 grid for indexing accessible points = 1.400000 m= 95915 mr = 130617 m= 39331 mr = 80220 m= 11554 mr = 32564 m= 2384 mr = 8963 m= 271 mr = 1689 m= 10 mr = 181 m= 0 mr = 3 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.240000 number of dielectric boundary points 70690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15384 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) : 2.154485 object centre at (A) : 25.29600 21.51350 22.18350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4526144 0.6121876 midg,1,midg; midg,igrid,midg -1.0787578E-02 0.2017003 1,midg,midg; igrid,midg,midg 0.3490214 0.1704658 gauss-seidel spectral radius is 0.9992984 estimated iterations to convergence 298 setup time was (sec) 2.560000 now iterating at: 06:24:03 rms-change max change #iterations 10.29228 450.6274 at 10iterations 6.110625 133.0354 at 20iterations 3.612530 81.64173 at 30iterations 2.131992 45.46822 at 40iterations 1.255071 22.82273 at 50iterations 0.7400935 12.92517 at 60iterations 0.4357603 8.101450 at 70iterations 0.2559095 4.317237 at 80iterations 0.1500478 2.841930 at 90iterations 8.8532209E-02 1.658876 at 100iterations 5.2178990E-02 0.9474182 at 110iterations 3.0944077E-02 0.5362625 at 120iterations 1.8595489E-02 0.3461418 at 130iterations 1.1387125E-02 0.2049065 at 140iterations 7.2355643E-03 0.1392365 at 150iterations 4.8030368E-03 0.1021919 at 160iterations 3.3832963E-03 6.6577911E-02 at 170iterations 2.5167041E-03 4.7981262E-02 at 180iterations finished qdiffx linear iterations at : 06:24:17 total time elapsed so far: 16.49000 # loops : 180 mean,max change (kT/e) : 2.5167041E-03 4.7981262E-02 energy calculations done at 16.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.66000 DelPhi exited at 06:24:18 16.665u 0.333s 0:17.41 97.5% 0+0k 0+0io 0pf+0w