Tue Oct 11 06:02:44 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 06:02:44 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7066997 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): 25.66500 72.09299 ymin,ymax (A): -18.77500 31.60000 zmin,zma (A): 3.885000 46.29800 x,y,z range (A): 46.42799 50.37500 42.41300 scale (grids/A): 0.7066997 object centre (A): 48.87900 6.412500 25.09150 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3759 centred at (gu) : 89.17392 90.18842 90.38184 assigned negative charge : -319.4310 centred at (gu) : 89.30244 90.12155 90.46577 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7196 nv = 96 ne = 84 npr = 42497 no. pairs analyzed = 42497 no. exposed pairs = 2581 no. arc points = 17478 no. surface atoms = 887 nbur = 1431 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 463 mr = 4180 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1601 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7961 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3879321E-08 7.0004993E-09 midg,1,midg; midg,igrid,midg 1.4881853E-08 8.4953051E-08 1,midg,midg; igrid,midg,midg 1.3167607E-07 -1.3127159E-08 gauss-seidel spectral radius is 0.9895653 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:02:45 rms-change max change #iterations 0.2049280 30.23788 at 10iterations 2.5855208E-02 4.163689 at 20iterations 3.4152048E-03 0.4544830 at 30iterations 5.7890592E-04 7.9597473E-02 at 40iterations 1.4663440E-04 1.7783165E-02 at 50iterations finished qdiffx linear iterations at : 06:02:48 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.4663440E-04 1.7783165E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 06:02:48 3.394u 0.184s 0:03.90 91.5% 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 06:02:48 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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: 2.120099 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): 25.66500 72.09299 ymin,ymax (A): -18.77500 31.60000 zmin,zma (A): 3.885000 46.29800 x,y,z range (A): 46.42799 50.37500 42.41300 scale (grids/A): 2.120099 object centre (A): 48.87900 6.412500 25.09150 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3759 centred at (gu) : 87.52177 90.56519 91.14550 assigned negative charge : -319.4310 centred at (gu) : 87.90735 90.36473 91.39730 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17478 grid for indexing accessible points = 1.400000 m= 31182 mr = 54517 m= 5960 mr = 23878 m= 546 mr = 4020 m= 15 mr = 293 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15784 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) : 0.7066997 object centre at (A) : 48.87900 6.412500 25.09150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9259648E-02 2.8094059E-02 midg,1,midg; midg,igrid,midg 3.9403003E-02 2.7715020E-02 1,midg,midg; igrid,midg,midg 4.4076670E-02 -5.1325101E-02 gauss-seidel spectral radius is 0.9988314 estimated iterations to convergence 232 setup time was (sec) 0.6200000 now iterating at: 06:02:49 rms-change max change #iterations 4.686622 189.7509 at 10iterations 2.315565 82.10156 at 20iterations 1.149154 34.76326 at 30iterations 0.5709847 17.47328 at 40iterations 0.2844577 8.345352 at 50iterations 0.1410997 4.177848 at 60iterations 7.0006028E-02 2.275741 at 70iterations 3.4924485E-02 0.9865398 at 80iterations 1.7481390E-02 0.5320215 at 90iterations 8.7812617E-03 0.2787037 at 100iterations 4.4500483E-03 0.1482849 at 110iterations 2.3101263E-03 6.9306374E-02 at 120iterations finished qdiffx linear iterations at : 06:02:56 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.3101263E-03 6.9306374E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 06:02:57 7.903u 0.200s 0:08.38 96.6% 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 06:02:57 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.180149 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): 25.66500 72.09299 ymin,ymax (A): -18.77500 31.60000 zmin,zma (A): 3.885000 46.29800 x,y,z range (A): 46.42799 50.37500 42.41300 scale (grids/A): 3.180149 object centre (A): 48.87900 6.412500 25.09150 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.3759 centred at (gu) : 86.28256 90.84776 91.71828 assigned negative charge : -319.4310 centred at (gu) : 86.86115 90.54707 92.09595 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17478 grid for indexing accessible points = 1.400000 m= 96751 mr = 131004 m= 39777 mr = 80956 m= 11340 mr = 32932 m= 2199 mr = 8806 m= 262 mr = 1601 m= 18 mr = 175 m= 0 mr = 9 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15904 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) : 2.120099 object centre at (A) : 48.87900 6.412500 25.09150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1140123 0.2382509 midg,1,midg; midg,igrid,midg 0.2787831 0.1308518 1,midg,midg; igrid,midg,midg 0.4209484 -0.6182670 gauss-seidel spectral radius is 0.9992977 estimated iterations to convergence 298 setup time was (sec) 1.430000 now iterating at: 06:02:58 rms-change max change #iterations 10.37545 355.5478 at 10iterations 6.137939 150.6165 at 20iterations 3.634551 72.90995 at 30iterations 2.141020 42.24758 at 40iterations 1.260640 24.20194 at 50iterations 0.7419477 14.43378 at 60iterations 0.4360234 7.794998 at 70iterations 0.2559077 5.154382 at 80iterations 0.1501263 2.595043 at 90iterations 8.8083610E-02 1.545844 at 100iterations 5.1934071E-02 0.9132147 at 110iterations 3.0667590E-02 0.5808983 at 120iterations 1.8204300E-02 0.3108749 at 130iterations 1.1043675E-02 0.2014618 at 140iterations 6.8356628E-03 0.1327934 at 150iterations 4.3831547E-03 8.1817627E-02 at 160iterations 2.9625380E-03 6.3987732E-02 at 170iterations 2.1206380E-03 4.1938782E-02 at 180iterations finished qdiffx linear iterations at : 06:03:10 total time elapsed so far: 13.33000 # loops : 180 mean,max change (kT/e) : 2.1206380E-03 4.1938782E-02 energy calculations done at 13.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 06:03:11 13.474u 0.261s 0:14.18 96.8% 0+0k 0+0io 0pf+0w