Mon Oct 10 11:33:44 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 Mon Oct 10 2011 at 11:33:44 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7423781 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): -20.82600 24.66900 ymin,ymax (A): -7.913000 36.02400 zmin,zma (A): -3.429000 44.52500 x,y,z range (A): 45.49500 43.93700 47.95400 scale (grids/A): 0.7423781 object centre (A): 1.921499 14.05550 20.54800 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 88.84001 90.45918 90.19644 assigned negative charge : -324.1720 centred at (gu) : 88.87576 90.55270 90.38526 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8078 nv = 96 ne = 84 npr = 43409 no. pairs analyzed = 43409 no. exposed pairs = 2652 no. arc points = 19064 no. surface atoms = 902 nbur = 1215 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 597 mr = 4533 m= 7 mr = 140 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 64 time to turn everything in is 0.3400000 number of dielectric boundary points 4009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1576 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1157168E-08 -3.3499688E-07 midg,1,midg; midg,igrid,midg -1.4801866E-08 -2.3660073E-07 1,midg,midg; igrid,midg,midg -9.4377832E-08 -1.2494651E-07 gauss-seidel spectral radius is 0.9905462 estimated iterations to convergence 84 setup time was (sec) 0.5600000 now iterating at: 11:33:44 rms-change max change #iterations 0.2470890 30.96870 at 10iterations 3.3792682E-02 4.804260 at 20iterations 4.5931861E-03 0.6007273 at 30iterations 6.3087360E-04 7.8230858E-02 at 40iterations 8.2913284E-05 1.2382507E-02 at 50iterations finished qdiffx linear iterations at : 11:33:47 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 8.2913284E-05 1.2382507E-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) 3.580000 DelPhi exited at 11:33:48 3.580u 0.183s 0:04.29 87.6% 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 Mon Oct 10 2011 at 11:33:48 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.227134 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): -20.82600 24.66900 ymin,ymax (A): -7.913000 36.02400 zmin,zma (A): -3.429000 44.52500 x,y,z range (A): 45.49500 43.93700 47.95400 scale (grids/A): 2.227134 object centre (A): 1.921499 14.05550 20.54800 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 86.52000 91.37730 90.58897 assigned negative charge : -324.1720 centred at (gu) : 86.62733 91.65812 91.15571 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 84461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19064 grid for indexing accessible points = 1.400000 m= 34875 mr = 58238 m= 7923 mr = 26967 m= 914 mr = 5579 m= 30 mr = 578 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1735 time to turn everything in is 0.6700000 number of dielectric boundary points 36841 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15756 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) : 0.7423781 object centre at (A) : 1.921499 14.05550 20.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7961694E-04 -0.1441503 midg,1,midg; midg,igrid,midg -2.7094081E-02 -3.5223138E-02 1,midg,midg; igrid,midg,midg 2.9532951E-03 -6.2352843E-03 gauss-seidel spectral radius is 0.9989320 estimated iterations to convergence 242 setup time was (sec) 0.9800000 now iterating at: 11:33:49 rms-change max change #iterations 5.096517 199.7124 at 10iterations 2.586888 80.86638 at 20iterations 1.323533 39.51394 at 30iterations 0.6747953 18.83270 at 40iterations 0.3441559 10.81108 at 50iterations 0.1763415 5.012899 at 60iterations 9.0050407E-02 2.547611 at 70iterations 4.5865521E-02 1.266129 at 80iterations 2.3419062E-02 0.6208839 at 90iterations 1.1975300E-02 0.3677559 at 100iterations 6.1083268E-03 0.1618786 at 110iterations 3.1236452E-03 8.2268476E-02 at 120iterations finished qdiffx linear iterations at : 11:33:56 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 3.1236452E-03 8.2268476E-02 energy calculations done at 8.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 11:33:57 8.292u 0.228s 0:08.83 96.3% 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 11:33:57 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.340701 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): -20.82600 24.66900 ymin,ymax (A): -7.913000 36.02400 zmin,zma (A): -3.429000 44.52500 x,y,z range (A): 45.49500 43.93700 47.95400 scale (grids/A): 3.340701 object centre (A): 1.921499 14.05550 20.54800 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 84.78009 92.06593 90.88337 assigned negative charge : -324.1720 centred at (gu) : 84.94102 92.48717 91.73357 start vw surface at 0.1400000 fill in re-entrant regions at 0.9500000 boundary points on vw surface= 194249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19064 grid for indexing accessible points = 1.400000 m= 105422 mr = 140023 m= 47153 mr = 88089 m= 15427 mr = 39538 m= 3808 mr = 12452 m= 608 mr = 3060 m= 20 mr = 428 m= 0 mr = 2 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 5662 time to turn everything in is 2.130000 number of dielectric boundary points 83095 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.280000 number of grid points assigned charge 15824 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) : 2.227134 object centre at (A) : 1.921499 14.05550 20.54800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4656124E-02 -1.343175 midg,1,midg; midg,igrid,midg -0.2553942 -0.1539370 1,midg,midg; igrid,midg,midg 9.1408864E-02 -0.1465198 gauss-seidel spectral radius is 0.9993208 estimated iterations to convergence 303 setup time was (sec) 2.440000 now iterating at: 11:33:59 rms-change max change #iterations 11.06547 298.2764 at 10iterations 6.500928 128.5587 at 20iterations 3.823241 65.96301 at 30iterations 2.246733 34.10108 at 40iterations 1.317808 22.39978 at 50iterations 0.7734742 13.01613 at 60iterations 0.4550572 7.432053 at 70iterations 0.2668099 4.283592 at 80iterations 0.1565505 2.510841 at 90iterations 9.1988787E-02 1.463078 at 100iterations 5.3913239E-02 0.8453239 at 110iterations 3.1699747E-02 0.5371017 at 120iterations 1.8624684E-02 0.2944984 at 130iterations 1.0924106E-02 0.1819572 at 140iterations 6.4158305E-03 0.1044140 at 150iterations 3.7722504E-03 5.5841446E-02 at 160iterations 2.2126285E-03 3.4450531E-02 at 170iterations 1.2998744E-03 2.0614624E-02 at 180iterations finished qdiffx linear iterations at : 11:34:11 total time elapsed so far: 13.81000 # loops : 180 mean,max change (kT/e) : 1.2998744E-03 2.0614624E-02 energy calculations done at 13.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 11:34:11 14.009u 0.202s 0:14.48 98.0% 0+0k 0+0io 0pf+0w