Mon Oct 10 14:06:13 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 14:06:14 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2328 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6677170 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): -11.98200 33.04700 ymin,ymax (A): -22.12400 29.91900 zmin,zma (A): -10.74300 42.57300 x,y,z range (A): 45.02900 52.04300 53.31600 scale (grids/A): 0.6677170 object centre (A): 10.53250 3.897499 15.91500 number of atom coordinates read : 2328 total number of charged atoms : 2188 net assigned charge : 3.500003 assigned positive charge : 347.6904 centred at (gu) : 91.54103 90.77863 90.15175 assigned negative charge : -344.1908 centred at (gu) : 91.46089 90.75243 89.92071 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 45413 no. pairs analyzed = 45413 no. exposed pairs = 3006 no. arc points = 21400 no. surface atoms = 1024 nbur = 1304 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3859 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2042 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8223 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8563048E-08 6.0420575E-08 midg,1,midg; midg,igrid,midg 4.2998973E-09 1.8868514E-08 1,midg,midg; igrid,midg,midg -4.6793041E-09 3.7805780E-08 gauss-seidel spectral radius is 0.9883571 estimated iterations to convergence 76 setup time was (sec) 0.6000000 now iterating at: 14:06:14 rms-change max change #iterations 0.1638348 25.48669 at 10iterations 1.7770916E-02 2.523770 at 20iterations 1.9528231E-03 0.2850780 at 30iterations 2.5142642E-04 3.5259247E-02 at 40iterations 6.4772787E-05 1.1435509E-02 at 50iterations finished qdiffx linear iterations at : 14:06:17 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 6.4772787E-05 1.1435509E-02 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:06:18 3.578u 0.173s 0:04.28 87.3% 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 14:06:18 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2328 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.003151 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): -11.98200 33.04700 ymin,ymax (A): -22.12400 29.91900 zmin,zma (A): -10.74300 42.57300 x,y,z range (A): 45.02900 52.04300 53.31600 scale (grids/A): 2.003151 object centre (A): 10.53250 3.897499 15.91500 number of atom coordinates read : 2328 total number of charged atoms : 2188 net assigned charge : 3.500003 assigned positive charge : 347.6904 centred at (gu) : 94.62281 92.33560 90.45490 assigned negative charge : -344.1908 centred at (gu) : 94.38245 92.25716 89.76186 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21400 grid for indexing accessible points = 1.400000 m= 27972 mr = 53041 m= 4570 mr = 20287 m= 325 mr = 2810 m= 4 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.6300000 number of dielectric boundary points 34084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17324 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) : 0.6677170 object centre at (A) : 10.53250 3.897499 15.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1725693E-02 5.9622135E-03 midg,1,midg; midg,igrid,midg 3.9516844E-02 2.8424770E-02 1,midg,midg; igrid,midg,midg -1.5763706E-02 9.9999281E-03 gauss-seidel spectral radius is 0.9987423 estimated iterations to convergence 223 setup time was (sec) 0.9500000 now iterating at: 14:06:19 rms-change max change #iterations 4.385414 174.2580 at 10iterations 2.113709 76.51549 at 20iterations 1.022438 30.38215 at 30iterations 0.4933708 15.55612 at 40iterations 0.2383853 8.100358 at 50iterations 0.1150175 3.411421 at 60iterations 5.5881444E-02 1.834866 at 70iterations 2.7003806E-02 0.8438654 at 80iterations 1.3050438E-02 0.4919968 at 90iterations 6.3148816E-03 0.1987395 at 100iterations 3.0534139E-03 9.4904900E-02 at 110iterations 1.4761047E-03 4.0960312E-02 at 120iterations finished qdiffx linear iterations at : 14:06:26 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.4761047E-03 4.0960312E-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) 7.970000 DelPhi exited at 14:06:27 7.971u 0.181s 0:08.59 94.8% 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 14:06:27 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2328 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: 3.004726 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): -11.98200 33.04700 ymin,ymax (A): -22.12400 29.91900 zmin,zma (A): -10.74300 42.57300 x,y,z range (A): 45.02900 52.04300 53.31600 scale (grids/A): 3.004726 object centre (A): 10.53250 3.897499 15.91500 number of atom coordinates read : 2328 total number of charged atoms : 2188 net assigned charge : 3.500003 assigned positive charge : 347.6904 centred at (gu) : 96.93392 93.50336 90.68233 assigned negative charge : -344.1908 centred at (gu) : 96.57364 93.38573 89.64285 start vw surface at 0.1300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 179245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21400 grid for indexing accessible points = 1.400000 m= 90360 mr = 128660 m= 32953 mr = 73471 m= 8310 mr = 26157 m= 1469 mr = 6130 m= 149 mr = 1073 m= 2 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 303 time to turn everything in is 1.540000 number of dielectric boundary points 76891 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 17504 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) : 2.003151 object centre at (A) : 10.53250 3.897499 15.91500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3545574 -9.5034048E-02 midg,1,midg; midg,igrid,midg 0.5525349 0.1003449 1,midg,midg; igrid,midg,midg -0.2301204 0.1004885 gauss-seidel spectral radius is 0.9992900 estimated iterations to convergence 296 setup time was (sec) 1.850000 now iterating at: 14:06:29 rms-change max change #iterations 10.17060 455.0120 at 10iterations 6.005254 158.9105 at 20iterations 3.543173 67.18466 at 30iterations 2.075347 41.75384 at 40iterations 1.220446 23.47615 at 50iterations 0.7152468 13.55338 at 60iterations 0.4185030 8.132366 at 70iterations 0.2439459 4.495335 at 80iterations 0.1423345 2.483520 at 90iterations 8.3107583E-02 1.597827 at 100iterations 4.8467971E-02 0.9170990 at 110iterations 2.8208887E-02 0.4896171 at 120iterations 1.6414339E-02 0.3175836 at 130iterations 9.5633073E-03 0.1641216 at 140iterations 5.5686804E-03 9.9802971E-02 at 150iterations 3.2418531E-03 5.8249474E-02 at 160iterations 1.8898381E-03 3.5328388E-02 at 170iterations 1.1008655E-03 1.8413544E-02 at 180iterations finished qdiffx linear iterations at : 14:06:40 total time elapsed so far: 13.12000 # loops : 180 mean,max change (kT/e) : 1.1008655E-03 1.8413544E-02 energy calculations done at 13.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 14:06:41 13.331u 0.205s 0:14.04 96.3% 0+0k 0+0io 0pf+0w