Mon Oct 10 11:18:51 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 11:18:52 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: 228 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7469576 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): -20.91300 24.64100 ymin,ymax (A): -8.183001 36.21300 zmin,zma (A): -3.494000 44.16600 x,y,z range (A): 45.55400 44.39600 47.66000 scale (grids/A): 0.7469576 object centre (A): 1.863999 14.01500 20.33600 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) : 88.82758 90.48713 90.24804 assigned negative charge : -323.3720 centred at (gu) : 88.84679 90.57404 90.42696 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8152 nv = 96 ne = 84 npr = 43649 no. pairs analyzed = 43649 no. exposed pairs = 2774 no. arc points = 19231 no. surface atoms = 934 nbur = 1183 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 4500 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1501 ## 113 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6384261E-08 -3.5797007E-07 midg,1,midg; midg,igrid,midg -2.3827610E-08 -2.5212225E-07 1,midg,midg; igrid,midg,midg -1.2856273E-07 -1.2142591E-07 gauss-seidel spectral radius is 0.9906607 estimated iterations to convergence 84 setup time was (sec) 0.6200000 now iterating at: 11:18:53 rms-change max change #iterations 0.2559734 34.63216 at 10iterations 3.4933694E-02 4.382118 at 20iterations 4.7450825E-03 0.5999224 at 30iterations 6.5745885E-04 8.4815979E-02 at 40iterations 8.9497313E-05 1.0951996E-02 at 50iterations finished qdiffx linear iterations at : 11:18:56 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 8.9497313E-05 1.0951996E-02 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 11:18:57 4.582u 0.381s 0:05.25 94.4% 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 Mon Oct 10 2011 at 11:18:57 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: 228 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.240873 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): -20.91300 24.64100 ymin,ymax (A): -8.183001 36.21300 zmin,zma (A): -3.494000 44.16600 x,y,z range (A): 45.55400 44.39600 47.66000 scale (grids/A): 2.240873 object centre (A): 1.863999 14.01500 20.33600 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) : 86.48285 91.46125 90.74426 assigned negative charge : -323.3720 centred at (gu) : 86.54033 91.72211 91.28091 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19231 grid for indexing accessible points = 1.400000 m= 34384 mr = 58930 m= 7346 mr = 25948 m= 819 mr = 5089 m= 26 mr = 431 m= 0 mr = 6 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 37826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15769 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) : 0.7469576 object centre at (A) : 1.863999 14.01500 20.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8767938E-03 -0.1395175 midg,1,midg; midg,igrid,midg -2.6442206E-02 -3.4763362E-02 1,midg,midg; igrid,midg,midg -2.1295885E-02 -4.6744943E-03 gauss-seidel spectral radius is 0.9989443 estimated iterations to convergence 243 setup time was (sec) 1.060000 now iterating at: 11:18:58 rms-change max change #iterations 5.150689 193.8321 at 10iterations 2.631789 84.66946 at 20iterations 1.346068 40.23284 at 30iterations 0.6900979 20.20776 at 40iterations 0.3543295 10.14102 at 50iterations 0.1815637 5.712606 at 60iterations 9.3019620E-02 2.740561 at 70iterations 4.7581531E-02 1.259908 at 80iterations 2.4407320E-02 0.6493592 at 90iterations 1.2532956E-02 0.3233871 at 100iterations 6.4358204E-03 0.1907349 at 110iterations 3.2921922E-03 0.1045880 at 120iterations finished qdiffx linear iterations at : 11:19:08 total time elapsed so far: 11.13000 # loops : 120 mean,max change (kT/e) : 3.2921922E-03 0.1045880 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.29000 DelPhi exited at 11:19:09 11.296u 0.465s 0:12.11 97.0% 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 Mon Oct 10 2011 at 11:19:09 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 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.361309 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): -20.91300 24.64100 ymin,ymax (A): -8.183001 36.21300 zmin,zma (A): -3.494000 44.16600 x,y,z range (A): 45.55400 44.39600 47.66000 scale (grids/A): 3.361309 object centre (A): 1.863999 14.01500 20.33600 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) : 84.72432 92.19186 91.11639 assigned negative charge : -323.3720 centred at (gu) : 84.81059 92.58324 91.92142 start vw surface at 0.1100000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 196922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19231 grid for indexing accessible points = 1.400000 m= 105220 mr = 141755 m= 45093 mr = 87059 m= 14195 mr = 37241 m= 3121 mr = 11062 m= 424 mr = 2394 m= 22 mr = 271 m= 0 mr = 4 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.250000 number of dielectric boundary points 85211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 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) : 2.240873 object centre at (A) : 1.863999 14.01500 20.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9777740E-02 -1.171738 midg,1,midg; midg,igrid,midg -0.2388782 -0.1697316 1,midg,midg; igrid,midg,midg -0.2247319 -0.1522334 gauss-seidel spectral radius is 0.9993247 estimated iterations to convergence 304 setup time was (sec) 2.590000 now iterating at: 11:19:12 rms-change max change #iterations 11.18244 271.0167 at 10iterations 6.621045 127.3687 at 20iterations 3.931539 73.00650 at 30iterations 2.319166 44.25195 at 40iterations 1.372254 24.09551 at 50iterations 0.8100997 13.97025 at 60iterations 0.4773465 7.647507 at 70iterations 0.2824453 4.825697 at 80iterations 0.1659567 2.585608 at 90iterations 9.7922750E-02 1.868282 at 100iterations 5.7502855E-02 0.9234314 at 110iterations 3.3946887E-02 0.5463715 at 120iterations 1.9958435E-02 0.3011122 at 130iterations 1.1741615E-02 0.1897159 at 140iterations 6.9300863E-03 0.1067276 at 150iterations 4.0755924E-03 6.2580109E-02 at 160iterations 2.4059303E-03 4.0426254E-02 at 170iterations 1.4134747E-03 2.1553993E-02 at 180iterations finished qdiffx linear iterations at : 11:19:29 total time elapsed so far: 19.43000 # loops : 180 mean,max change (kT/e) : 1.4134747E-03 2.1553993E-02 energy calculations done at 19.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.58000 DelPhi exited at 11:19:29 19.589u 0.485s 0:20.45 98.0% 0+0k 0+0io 0pf+0w