Sun Oct 9 20:01:18 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 Sun Oct 9 2011 at 20:01:18 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5379 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5131457 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): 3.271000 69.09300 ymin,ymax (A): -8.900000 53.49000 zmin,zma (A): -2.042000 67.33400 x,y,z range (A): 65.82201 62.39000 69.37600 scale (grids/A): 0.5131457 object centre (A): 36.18200 22.29500 32.64600 number of atom coordinates read : 5379 total number of charged atoms : 5227 net assigned charge : 4.558032 assigned positive charge : 832.7363 centred at (gu) : 88.18587 89.26395 88.89309 assigned negative charge : -828.1841 centred at (gu) : 88.08017 89.27345 88.81426 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 9138 nv = 96 ne = 84 npr = 108008 no. pairs analyzed = 108008 no. exposed pairs = 6221 no. arc points = 43072 no. surface atoms = 2122 nbur = 3257 mkacc time = 0.2300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 313 mr = 5119 m= 0 mr = 9 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4248 ## 586 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 12177 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4722163E-10 2.5588187E-10 midg,1,midg; midg,igrid,midg 1.3801367E-10 4.2247764E-11 1,midg,midg; igrid,midg,midg -4.5009141E-10 2.6715852E-10 gauss-seidel spectral radius is 0.9806157 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 20:01:19 rms-change max change #iterations 8.1113175E-02 12.80400 at 10iterations 9.2033213E-03 1.421417 at 20iterations 3.6252534E-03 0.6183434 at 30iterations 1.6750138E-03 0.2847977 at 40iterations 7.8320841E-04 0.1308403 at 50iterations finished qdiffx linear iterations at : 20:01:21 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 7.8320841E-04 0.1308403 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 20:01:22 3.483u 0.194s 0:03.97 92.4% 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 Sun Oct 9 2011 at 20:01:22 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5379 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.539437 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): 3.271000 69.09300 ymin,ymax (A): -8.900000 53.49000 zmin,zma (A): -2.042000 67.33400 x,y,z range (A): 65.82201 62.39000 69.37600 scale (grids/A): 1.539437 object centre (A): 36.18200 22.29500 32.64600 number of atom coordinates read : 5379 total number of charged atoms : 5227 net assigned charge : 4.558032 assigned positive charge : 832.7363 centred at (gu) : 84.55585 87.79064 86.67775 assigned negative charge : -828.1841 centred at (gu) : 84.24058 87.82002 86.44287 start vw surface at 0.2100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 104077 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 33222 mr = 75328 m= 3062 mr = 23282 m= 55 mr = 1442 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 40362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 573 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 39384 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) : 0.5131457 object centre at (A) : 36.18200 22.29500 32.64600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4028996E-02 2.6696689E-02 midg,1,midg; midg,igrid,midg 1.4384884E-02 5.6624711E-03 1,midg,midg; igrid,midg,midg -1.6800888E-02 3.5810221E-03 gauss-seidel spectral radius is 0.9981750 estimated iterations to convergence 186 setup time was (sec) 0.9800000 now iterating at: 20:01:23 rms-change max change #iterations 4.221025 150.4541 at 10iterations 1.755587 61.33577 at 20iterations 0.7350358 23.48861 at 30iterations 0.3059937 8.782356 at 40iterations 0.1289337 3.719210 at 50iterations 5.5003863E-02 1.724530 at 60iterations 2.4561096E-02 0.7604218 at 70iterations 1.2125285E-02 0.4304955 at 80iterations 7.1378709E-03 0.2423782 at 90iterations 4.7898255E-03 0.1562767 at 100iterations 3.4815946E-03 0.1124315 at 110iterations 2.6078115E-03 8.3171844E-02 at 120iterations finished qdiffx linear iterations at : 20:01:30 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.6078115E-03 8.3171844E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 20:01:30 7.744u 0.226s 0:08.24 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 Sun Oct 9 2011 at 20:01:30 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: 338 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5379 !!! WARNING: HIR 341 has a net charge of 0.5140 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.309156 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): 3.271000 69.09300 ymin,ymax (A): -8.900000 53.49000 zmin,zma (A): -2.042000 67.33400 x,y,z range (A): 65.82201 62.39000 69.37600 scale (grids/A): 2.309156 object centre (A): 36.18200 22.29500 32.64600 number of atom coordinates read : 5379 total number of charged atoms : 5227 net assigned charge : 4.558032 assigned positive charge : 832.7363 centred at (gu) : 81.83334 86.68552 85.01617 assigned negative charge : -828.1841 centred at (gu) : 81.36079 86.72995 84.66421 start vw surface at 0.2000000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 242866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 116963 mr = 184005 m= 31952 mr = 94470 m= 4600 mr = 23931 m= 259 mr = 2882 m= 4 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.720000 number of dielectric boundary points 91241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 41698 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) : 1.539437 object centre at (A) : 36.18200 22.29500 32.64600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3234669 0.8287802 midg,1,midg; midg,igrid,midg 0.2298242 5.1221173E-02 1,midg,midg; igrid,midg,midg -0.3874869 5.7437025E-02 gauss-seidel spectral radius is 0.9991819 estimated iterations to convergence 276 setup time was (sec) 2.040000 now iterating at: 20:01:32 rms-change max change #iterations 11.11162 267.8889 at 10iterations 6.379442 127.3138 at 20iterations 3.622433 73.44414 at 30iterations 2.051605 39.57211 at 40iterations 1.156946 23.72448 at 50iterations 0.6516335 11.64543 at 60iterations 0.3673002 6.724323 at 70iterations 0.2067325 3.960152 at 80iterations 0.1161075 2.036680 at 90iterations 6.5744825E-02 1.354527 at 100iterations 3.7489604E-02 0.7223511 at 110iterations 2.1778028E-02 0.4104004 at 120iterations 1.3163238E-02 0.2893829 at 130iterations 8.4271394E-03 0.1706581 at 140iterations 5.8046100E-03 0.1197052 at 150iterations 4.3050088E-03 8.7747574E-02 at 160iterations 3.3688096E-03 6.6604614E-02 at 170iterations 2.7214577E-03 5.2787781E-02 at 180iterations finished qdiffx linear iterations at : 20:01:43 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 2.7214577E-03 5.2787781E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 20:01:44 12.900u 0.248s 0:13.45 97.6% 0+0k 0+0io 0pf+0w