Sun Oct 9 20:00:52 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+sph.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 = amb.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 20:00:52 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5379 !!! 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= 0.1400000 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 : 4.530032 assigned positive charge : 827.4521 centred at (gu) : 88.17606 89.25864 88.89718 assigned negative charge : -822.9282 centred at (gu) : 88.07128 89.27081 88.81982 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 0.4800000 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 -2.3891331E-10 2.5082553E-10 midg,1,midg; midg,igrid,midg 1.4781827E-10 3.4536589E-11 1,midg,midg; igrid,midg,midg -4.4356244E-10 2.6283975E-10 gauss-seidel spectral radius is 0.9806157 estimated iterations to convergence 59 setup time was (sec) 0.7100000 now iterating at: 20:00:53 rms-change max change #iterations 7.9349555E-02 11.59405 at 10iterations 9.5712719E-03 1.514038 at 20iterations 3.8604343E-03 0.6606674 at 30iterations 1.7858798E-03 0.3039284 at 40iterations 8.3528360E-04 0.1395531 at 50iterations finished qdiffx linear iterations at : 20:00:55 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.3528360E-04 0.1395531 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 20:00:56 3.403u 0.149s 0:04.00 88.5% 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 Sun Oct 9 2011 at 20:00:56 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5379 !!! 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 : 4.530032 assigned positive charge : 827.4521 centred at (gu) : 84.52634 87.77467 86.69006 assigned negative charge : -822.9282 centred at (gu) : 84.21387 87.81209 86.45954 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 = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 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 0.8100000 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 -1.3463119E-02 2.6617384E-02 midg,1,midg; midg,igrid,midg 1.4472078E-02 5.3679533E-03 1,midg,midg; igrid,midg,midg -1.6481819E-02 3.4925377E-03 gauss-seidel spectral radius is 0.9981750 estimated iterations to convergence 186 setup time was (sec) 0.9700000 now iterating at: 20:00:57 rms-change max change #iterations 4.189484 150.4541 at 10iterations 1.741426 61.62395 at 20iterations 0.7293553 23.48873 at 30iterations 0.3037922 8.796677 at 40iterations 0.1281228 3.735240 at 50iterations 5.4849327E-02 1.706532 at 60iterations 2.4734827E-02 0.7652435 at 70iterations 1.2429936E-02 0.4409941 at 80iterations 7.4722008E-03 0.2515411 at 90iterations 5.0810976E-03 0.1655731 at 100iterations 3.7147487E-03 0.1194077 at 110iterations 2.7873321E-03 8.9103699E-02 at 120iterations finished qdiffx linear iterations at : 20:01:03 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 2.7873321E-03 8.9103699E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 20:01:04 7.352u 0.179s 0:07.89 95.3% 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 Sun Oct 9 2011 at 20:01:04 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5379 !!! 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 : 4.530032 assigned positive charge : 827.4521 centred at (gu) : 81.78905 86.66151 85.03465 assigned negative charge : -822.9282 centred at (gu) : 81.32076 86.71804 84.68922 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 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 1.740000 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 1.890000 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 -0.3137475 0.8276314 midg,1,midg; midg,igrid,midg 0.2307091 4.6607491E-02 1,midg,midg; igrid,midg,midg -0.3811854 5.6143880E-02 gauss-seidel spectral radius is 0.9991819 estimated iterations to convergence 276 setup time was (sec) 2.070000 now iterating at: 20:01:06 rms-change max change #iterations 11.03029 267.9569 at 10iterations 6.333075 128.4350 at 20iterations 3.597480 72.34653 at 30iterations 2.037700 37.63238 at 40iterations 1.149561 23.50595 at 50iterations 0.6474820 11.72150 at 60iterations 0.3651038 6.610935 at 70iterations 0.2055487 3.928993 at 80iterations 0.1155208 2.041122 at 90iterations 6.5485232E-02 1.346058 at 100iterations 3.7425887E-02 0.7335815 at 110iterations 2.1837536E-02 0.4045868 at 120iterations 1.3303892E-02 0.2881660 at 130iterations 8.6108837E-03 0.1751766 at 140iterations 6.0027693E-03 0.1236725 at 150iterations 4.4975094E-03 9.1136932E-02 at 160iterations 3.5408633E-03 6.9454193E-02 at 170iterations 2.8703194E-03 5.5198669E-02 at 180iterations finished qdiffx linear iterations at : 20:01:17 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 2.8703194E-03 5.5198669E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 20:01:18 12.981u 0.212s 0:13.49 97.7% 0+0k 0+0io 0pf+0w