Sun Oct 9 17:15:57 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 17:15:57 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5027 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5640497 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): 3.245000 64.97500 ymin,ymax (A): -8.570000 53.44800 zmin,zma (A): -1.178000 61.93700 x,y,z range (A): 61.73000 62.01800 63.11500 scale (grids/A): 0.5640497 object centre (A): 34.11000 22.43900 30.37950 number of atom coordinates read : 5027 total number of charged atoms : 4878 net assigned charge : 3.5047799E-02 assigned positive charge : 775.0879 centred at (gu) : 88.35705 89.24714 89.19949 assigned negative charge : -775.0586 centred at (gu) : 88.25354 89.28269 89.16916 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 10491 nv = 96 ne = 84 npr = 101958 no. pairs analyzed = 101958 no. exposed pairs = 5935 no. arc points = 40072 no. surface atoms = 2023 nbur = 3004 mkacc time = 0.2800000 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 = 1.540000 m= 507 mr = 6056 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 4920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4090 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6499274E-10 5.9042515E-10 midg,1,midg; midg,igrid,midg 1.0010417E-09 -6.2024036E-10 1,midg,midg; igrid,midg,midg -3.4195327E-09 1.5550555E-09 gauss-seidel spectral radius is 0.9839368 estimated iterations to convergence 65 setup time was (sec) 0.9000000 now iterating at: 17:15:58 rms-change max change #iterations 0.1194967 14.58913 at 10iterations 1.0750701E-02 1.340279 at 20iterations 2.8253542E-03 0.3161621 at 30iterations 1.3225749E-03 0.1382294 at 40iterations 6.5294025E-04 7.4969292E-02 at 50iterations finished qdiffx linear iterations at : 17:16:03 total time elapsed so far: 5.650000 # loops : 50 mean,max change (kT/e) : 6.5294025E-04 7.4969292E-02 energy calculations done at 5.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.830000 DelPhi exited at 17:16:03 5.831u 0.462s 0:06.54 96.1% 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 17:16:03 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5027 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.692149 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): 3.245000 64.97500 ymin,ymax (A): -8.570000 53.44800 zmin,zma (A): -1.178000 61.93700 x,y,z range (A): 61.73000 62.01800 63.11500 scale (grids/A): 1.692149 object centre (A): 34.11000 22.43900 30.37950 number of atom coordinates read : 5027 total number of charged atoms : 4878 net assigned charge : 3.5047799E-02 assigned positive charge : 775.0879 centred at (gu) : 85.06978 87.74014 87.59689 assigned negative charge : -775.0586 centred at (gu) : 84.76054 87.84833 87.50751 start vw surface at 0.1900000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 116753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40072 grid for indexing accessible points = 1.400000 m= 41239 mr = 84561 m= 5303 mr = 29953 m= 182 mr = 2972 m= 0 mr = 27 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 45964 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 3 charges are in solution ## iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 37597 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) : 0.5640497 object centre at (A) : 34.11000 22.43900 30.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0785561E-02 -2.8781438E-02 midg,1,midg; midg,igrid,midg 1.7304717E-02 9.8297792E-03 1,midg,midg; igrid,midg,midg -2.0505859E-02 2.7754711E-02 gauss-seidel spectral radius is 0.9985006 estimated iterations to convergence 205 setup time was (sec) 1.450000 now iterating at: 17:16:05 rms-change max change #iterations 5.030900 194.0145 at 10iterations 2.264534 64.72095 at 20iterations 1.024566 28.67097 at 30iterations 0.4650416 12.90930 at 40iterations 0.2101556 5.783501 at 50iterations 9.5604017E-02 2.629982 at 60iterations 4.3630321E-02 1.298532 at 70iterations 2.0327397E-02 0.5312490 at 80iterations 9.8921452E-03 0.2947464 at 90iterations 5.2978308E-03 0.1455688 at 100iterations 3.2346351E-03 9.3620300E-02 at 110iterations 2.2463929E-03 5.7850838E-02 at 120iterations finished qdiffx linear iterations at : 17:16:17 total time elapsed so far: 13.44000 # loops : 120 mean,max change (kT/e) : 2.2463929E-03 5.7850838E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 17:16:18 13.614u 0.521s 0:14.41 98.0% 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 17:16:18 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5027 !!! WARNING: ASL 284 has a net charge of -0.1000 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.538224 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): 3.245000 64.97500 ymin,ymax (A): -8.570000 53.44800 zmin,zma (A): -1.178000 61.93700 x,y,z range (A): 61.73000 62.01800 63.11500 scale (grids/A): 2.538224 object centre (A): 34.11000 22.43900 30.37950 number of atom coordinates read : 5027 total number of charged atoms : 4878 net assigned charge : 3.5047799E-02 assigned positive charge : 775.0879 centred at (gu) : 82.60455 86.60973 86.39493 assigned negative charge : -775.0586 centred at (gu) : 82.14068 86.77246 86.26119 start vw surface at 0.1900000 fill in re-entrant regions at 0.7500000 boundary points on vw surface= 271168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40072 grid for indexing accessible points = 1.400000 m= 138203 mr = 205729 m= 45135 mr = 112850 m= 8798 mr = 35168 m= 817 mr = 6166 m= 27 mr = 421 m= 0 mr = 4 time to grow re-entrant surface = 1.600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.530000 number of dielectric boundary points 103810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 2.720000 number of grid points assigned charge 38994 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) : 1.692149 object centre at (A) : 34.11000 22.43900 30.37950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4815252 -0.6733162 midg,1,midg; midg,igrid,midg -1.4333952E-02 1.1689676E-03 1,midg,midg; igrid,midg,midg -0.4041244 0.3149167 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 2.960000 now iterating at: 17:16:21 rms-change max change #iterations 12.62484 320.8933 at 10iterations 7.487413 141.8399 at 20iterations 4.421337 95.27612 at 30iterations 2.600295 45.55228 at 40iterations 1.523551 28.74331 at 50iterations 0.8903740 15.13448 at 60iterations 0.5188050 7.839434 at 70iterations 0.3023227 4.633606 at 80iterations 0.1758349 2.944138 at 90iterations 0.1021349 1.727905 at 100iterations 5.9348997E-02 0.9497700 at 110iterations 3.4652177E-02 0.5602283 at 120iterations 2.0282589E-02 0.3182244 at 130iterations 1.2038225E-02 0.1945801 at 140iterations 7.3115896E-03 0.1126709 at 150iterations 4.6420670E-03 7.8193665E-02 at 160iterations 3.1463483E-03 4.9776077E-02 at 170iterations 2.2992585E-03 3.4584045E-02 at 180iterations finished qdiffx linear iterations at : 17:16:42 total time elapsed so far: 24.11000 # loops : 180 mean,max change (kT/e) : 2.2992585E-03 3.4584045E-02 energy calculations done at 24.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.27000 DelPhi exited at 17:16:43 24.275u 0.560s 0:25.15 98.7% 0+0k 0+0io 0pf+0w