Tue Oct 11 03:49:10 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 03:49:10 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3236 !!! WARNING: HIQ 79 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: GLU 287 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6061947 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): -10.41800 36.97700 ymin,ymax (A): -27.42400 21.46800 zmin,zma (A): -13.29600 45.43100 x,y,z range (A): 47.39500 48.89200 58.72700 scale (grids/A): 0.6061947 object centre (A): 13.27950 -2.978000 16.06750 number of atom coordinates read : 3236 total number of charged atoms : 2813 net assigned charge : -5.320980 assigned positive charge : 452.9483 centred at (gu) : 89.70876 91.15965 92.29510 assigned negative charge : -458.2701 centred at (gu) : 89.51877 91.13525 92.17223 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7113 nv = 96 ne = 84 npr = 61291 no. pairs analyzed = 61291 no. exposed pairs = 3506 no. arc points = 24203 no. surface atoms = 1176 nbur = 2060 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 4056 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3800000 number of dielectric boundary points 3364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2430 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6049316E-09 5.8732823E-09 midg,1,midg; midg,igrid,midg -3.2255674E-09 -2.0900688E-09 1,midg,midg; igrid,midg,midg -1.3826746E-08 6.2801502E-09 gauss-seidel spectral radius is 0.9859369 estimated iterations to convergence 69 setup time was (sec) 0.6100000 now iterating at: 03:49:10 rms-change max change #iterations 0.1266272 17.30288 at 10iterations 1.1056514E-02 1.662550 at 20iterations 1.0298248E-03 0.1437035 at 30iterations 1.3267773E-04 1.8283367E-02 at 40iterations 3.0733132E-05 4.6677589E-03 at 50iterations finished qdiffx linear iterations at : 03:49:13 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 3.0733132E-05 4.6677589E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 03:49:14 3.496u 0.185s 0:04.01 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 03:49:14 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3236 !!! WARNING: HIQ 79 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: GLU 287 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.818584 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): -10.41800 36.97700 ymin,ymax (A): -27.42400 21.46800 zmin,zma (A): -13.29600 45.43100 x,y,z range (A): 47.39500 48.89200 58.72700 scale (grids/A): 1.818584 object centre (A): 13.27950 -2.978000 16.06750 number of atom coordinates read : 3236 total number of charged atoms : 2813 net assigned charge : -5.320980 assigned positive charge : 452.9483 centred at (gu) : 89.12578 93.47823 96.88467 assigned negative charge : -458.2701 centred at (gu) : 88.55593 93.40504 96.51611 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 77548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24203 grid for indexing accessible points = 1.400000 m= 27456 mr = 55131 m= 3759 mr = 20437 m= 166 mr = 2251 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3517 time to turn everything in is 0.5900000 number of dielectric boundary points 31071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 21966 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) : 0.6061947 object centre at (A) : 13.27950 -2.978000 16.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4519251E-02 -4.1778965E-04 midg,1,midg; midg,igrid,midg -1.0155574E-02 -2.6821990E-02 1,midg,midg; igrid,midg,midg -1.6559239E-02 2.6714921E-02 gauss-seidel spectral radius is 0.9985347 estimated iterations to convergence 207 setup time was (sec) 0.8900000 now iterating at: 03:49:15 rms-change max change #iterations 4.290050 176.1035 at 10iterations 1.949991 69.29695 at 20iterations 0.8917873 31.21087 at 30iterations 0.4074770 13.96392 at 40iterations 0.1861008 6.864914 at 50iterations 8.4719613E-02 2.671561 at 60iterations 3.8882416E-02 1.224236 at 70iterations 1.7781487E-02 0.5387592 at 80iterations 8.0977939E-03 0.2564182 at 90iterations 3.7305050E-03 0.1193797 at 100iterations 1.7281825E-03 5.8643341E-02 at 110iterations 8.0663688E-04 2.4917603E-02 at 120iterations finished qdiffx linear iterations at : 03:49:23 total time elapsed so far: 8.870000 # loops : 120 mean,max change (kT/e) : 8.0663688E-04 2.4917603E-02 energy calculations done at 8.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.070000 DelPhi exited at 03:49:23 9.073u 0.206s 0:09.71 95.4% 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 03:49:23 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3236 !!! WARNING: HIQ 79 has a net charge of 0.5140 !!! WARNING: SEP 233 has a net charge of -0.4750 !!! WARNING: GLU 287 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.727876 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): -10.41800 36.97700 ymin,ymax (A): -27.42400 21.46800 zmin,zma (A): -13.29600 45.43100 x,y,z range (A): 47.39500 48.89200 58.72700 scale (grids/A): 2.727876 object centre (A): 13.27950 -2.978000 16.06750 number of atom coordinates read : 3236 total number of charged atoms : 2813 net assigned charge : -5.320980 assigned positive charge : 452.9483 centred at (gu) : 88.68832 95.21717 100.3269 assigned negative charge : -458.2701 centred at (gu) : 87.83387 95.10747 99.77427 start vw surface at 0.1800000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 179439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24203 grid for indexing accessible points = 1.400000 m= 90891 mr = 133249 m= 30948 mr = 75075 m= 6427 mr = 24964 m= 701 mr = 4756 m= 28 mr = 424 m= 0 mr = 7 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 11619 time to turn everything in is 1.470000 number of dielectric boundary points 69959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 22504 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) : 1.818584 object centre at (A) : 13.27950 -2.978000 16.06750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.054429 0.2559735 midg,1,midg; midg,igrid,midg -0.1285311 -0.3934189 1,midg,midg; igrid,midg,midg -0.1737920 0.2787400 gauss-seidel spectral radius is 0.9992302 estimated iterations to convergence 285 setup time was (sec) 1.790000 now iterating at: 03:49:25 rms-change max change #iterations 10.16860 371.3796 at 10iterations 5.878380 150.2066 at 20iterations 3.382959 78.01052 at 30iterations 1.941888 39.64065 at 40iterations 1.109322 21.26795 at 50iterations 0.6349899 11.42492 at 60iterations 0.3620705 6.835320 at 70iterations 0.2066667 3.712227 at 80iterations 0.1177089 2.207367 at 90iterations 6.7127906E-02 1.224529 at 100iterations 3.8339425E-02 0.7411690 at 110iterations 2.1825572E-02 0.3776045 at 120iterations 1.2453185E-02 0.2189093 at 130iterations 7.1243518E-03 0.1444492 at 140iterations 4.0710787E-03 7.2261810E-02 at 150iterations 2.3502049E-03 4.0428162E-02 at 160iterations 1.3645504E-03 2.4302483E-02 at 170iterations 8.0714747E-04 1.5663147E-02 at 180iterations finished qdiffx linear iterations at : 03:49:37 total time elapsed so far: 13.23000 # loops : 180 mean,max change (kT/e) : 8.0714747E-04 1.5663147E-02 energy calculations done at 13.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 03:49:38 13.417u 0.214s 0:14.16 96.1% 0+0k 0+0io 0pf+0w