Mon Oct 10 12:11:11 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 Mon Oct 10 2011 at 12:11:11 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 209 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7353548 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): 40.86300 89.27500 ymin,ymax (A): -9.336000 35.47500 zmin,zma (A): 21.44600 68.60000 x,y,z range (A): 48.41200 44.81100 47.15400 scale (grids/A): 0.7353548 object centre (A): 65.06900 13.06950 45.02300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.44534 90.76202 90.17059 assigned negative charge : -323.3720 centred at (gu) : 89.47337 90.85433 90.33562 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7877 nv = 96 ne = 84 npr = 43580 no. pairs analyzed = 43580 no. exposed pairs = 2689 no. arc points = 18774 no. surface atoms = 910 nbur = 1207 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 563 mr = 4402 m= 3 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2600000 number of dielectric boundary points 3927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1579 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 8376 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0772485E-08 -2.6350972E-07 midg,1,midg; midg,igrid,midg -1.2416116E-08 -2.1417769E-07 1,midg,midg; igrid,midg,midg -8.0238003E-08 -1.1293917E-07 gauss-seidel spectral radius is 0.9903649 estimated iterations to convergence 83 setup time was (sec) 0.5200000 now iterating at: 12:11:12 rms-change max change #iterations 0.2373800 41.57948 at 10iterations 3.1575572E-02 4.572166 at 20iterations 4.1481182E-03 0.5133171 at 30iterations 5.6401372E-04 7.8937531E-02 at 40iterations 7.5564196E-05 9.3460083E-03 at 50iterations finished qdiffx linear iterations at : 12:11:16 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 7.5564196E-05 9.3460083E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.380000 DelPhi exited at 12:11:16 4.380u 0.399s 0:05.28 90.3% 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 12:11:16 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 209 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.206064 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): 40.86300 89.27500 ymin,ymax (A): -9.336000 35.47500 zmin,zma (A): 21.44600 68.60000 x,y,z range (A): 48.41200 44.81100 47.15400 scale (grids/A): 2.206064 object centre (A): 65.06900 13.06950 45.02300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.33595 92.28616 90.51196 assigned negative charge : -323.3720 centred at (gu) : 88.42007 92.56285 91.00707 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82866 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18774 grid for indexing accessible points = 1.400000 m= 33783 mr = 57407 m= 7409 mr = 25836 m= 764 mr = 5187 m= 20 mr = 428 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.6900000 number of dielectric boundary points 35982 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15757 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) : 0.7353548 object centre at (A) : 65.06900 13.06950 45.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0773493E-02 -0.1265332 midg,1,midg; midg,igrid,midg -2.4815591E-02 -4.5202345E-02 1,midg,midg; igrid,midg,midg 6.2205130E-03 -5.5090054E-03 gauss-seidel spectral radius is 0.9989160 estimated iterations to convergence 240 setup time was (sec) 1.030000 now iterating at: 12:11:18 rms-change max change #iterations 5.023563 195.3386 at 10iterations 2.541049 84.40366 at 20iterations 1.288165 36.39616 at 30iterations 0.6559203 19.50110 at 40iterations 0.3323921 10.01947 at 50iterations 0.1688183 5.057384 at 60iterations 8.5949369E-02 2.462984 at 70iterations 4.3689497E-02 1.304937 at 80iterations 2.2200767E-02 0.6066380 at 90iterations 1.1263479E-02 0.3303351 at 100iterations 5.7427464E-03 0.1792974 at 110iterations 2.9204686E-03 8.3525658E-02 at 120iterations finished qdiffx linear iterations at : 12:11:27 total time elapsed so far: 10.57000 # loops : 120 mean,max change (kT/e) : 2.9204686E-03 8.3525658E-02 energy calculations done at 10.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.74000 DelPhi exited at 12:11:28 10.743u 0.434s 0:11.67 95.7% 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 12:11:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 209 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.309097 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): 40.86300 89.27500 ymin,ymax (A): -9.336000 35.47500 zmin,zma (A): 21.44600 68.60000 x,y,z range (A): 48.41200 44.81100 47.15400 scale (grids/A): 3.309097 object centre (A): 65.06900 13.06950 45.02300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 87.50375 93.42924 90.76793 assigned negative charge : -323.3720 centred at (gu) : 87.63013 93.84427 91.51058 start vw surface at 0.1100000 fill in re-entrant regions at 0.8600000 boundary points on vw surface= 190999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18774 grid for indexing accessible points = 1.400000 m= 102707 mr = 138318 m= 44349 mr = 85485 m= 14236 mr = 36912 m= 3111 mr = 11327 m= 396 mr = 2397 m= 24 mr = 237 m= 0 mr = 8 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 1175 time to turn everything in is 2.180000 number of dielectric boundary points 81138 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 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) : 2.206064 object centre at (A) : 65.06900 13.06950 45.02300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1112362 -1.215968 midg,1,midg; midg,igrid,midg -0.2370106 -0.2426229 1,midg,midg; igrid,midg,midg -6.4823449E-02 -4.2551126E-02 gauss-seidel spectral radius is 0.9993162 estimated iterations to convergence 302 setup time was (sec) 2.510000 now iterating at: 12:11:31 rms-change max change #iterations 10.89018 432.8497 at 10iterations 6.405138 108.1425 at 20iterations 3.773217 68.17064 at 30iterations 2.214580 38.43363 at 40iterations 1.303563 23.20920 at 50iterations 0.7652001 12.59798 at 60iterations 0.4487561 6.909973 at 70iterations 0.2636132 4.651295 at 80iterations 0.1547006 2.597894 at 90iterations 9.0772703E-02 1.384460 at 100iterations 5.3175692E-02 0.9663067 at 110iterations 3.1204334E-02 0.5225384 at 120iterations 1.8314866E-02 0.2888832 at 130iterations 1.0758375E-02 0.1763926 at 140iterations 6.3042203E-03 0.1087570 at 150iterations 3.6990689E-03 5.6644440E-02 at 160iterations 2.1742161E-03 3.5939217E-02 at 170iterations 1.2771075E-03 1.9550323E-02 at 180iterations finished qdiffx linear iterations at : 12:11:47 total time elapsed so far: 18.69000 # loops : 180 mean,max change (kT/e) : 1.2771075E-03 1.9550323E-02 energy calculations done at 18.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.84000 DelPhi exited at 12:11:48 18.848u 0.496s 0:19.68 98.2% 0+0k 0+0io 0pf+0w