Sun Oct 16 15:03:08 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 16 2011 at 15:03:08 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6203063 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): 14.11400 71.50500 ymin,ymax (A): 4.319000 51.78500 zmin,zma (A): 7.626000 63.62800 x,y,z range (A): 57.39101 47.46600 56.00200 scale (grids/A): 0.6203063 object centre (A): 42.80950 28.05200 35.62700 number of atom coordinates read : 2893 total number of charged atoms : 2752 net assigned charge : -1.985969 assigned positive charge : 436.4400 centred at (gu) : 89.02262 90.28823 90.88363 assigned negative charge : -438.4272 centred at (gu) : 88.96201 90.37069 90.92271 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7523 nv = 96 ne = 84 npr = 57600 no. pairs analyzed = 57600 no. exposed pairs = 3842 no. arc points = 27340 no. surface atoms = 1309 nbur = 1584 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3908 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2200000 number of dielectric boundary points 3975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2666 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9147 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1650361E-09 -5.4436735E-09 midg,1,midg; midg,igrid,midg 4.3743587E-09 -8.3181870E-09 1,midg,midg; igrid,midg,midg -7.6124920E-09 2.4344249E-09 gauss-seidel spectral radius is 0.9865748 estimated iterations to convergence 71 setup time was (sec) 0.4900000 now iterating at: 15:03:09 rms-change max change #iterations 0.1353131 20.11552 at 10iterations 1.2329889E-02 1.769579 at 20iterations 1.1390001E-03 0.1588840 at 30iterations 1.0666918E-04 1.4418602E-02 at 40iterations 1.0894380E-05 1.5711784E-03 at 50iterations finished qdiffx linear iterations at : 15:03:12 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 1.0894380E-05 1.5711784E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 15:03:13 4.427u 0.316s 0:05.01 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 Sun Oct 16 2011 at 15:03:13 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.860919 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): 14.11400 71.50500 ymin,ymax (A): 4.319000 51.78500 zmin,zma (A): 7.626000 63.62800 x,y,z range (A): 57.39101 47.46600 56.00200 scale (grids/A): 1.860919 object centre (A): 42.80950 28.05200 35.62700 number of atom coordinates read : 2893 total number of charged atoms : 2752 net assigned charge : -1.985969 assigned positive charge : 436.4400 centred at (gu) : 87.06665 90.86392 92.65015 assigned negative charge : -438.4272 centred at (gu) : 86.88558 91.11168 92.76772 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27340 grid for indexing accessible points = 1.400000 m= 28237 mr = 54318 m= 4168 mr = 20087 m= 245 mr = 2464 m= 0 mr = 81 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 567 time to turn everything in is 0.4300000 number of dielectric boundary points 36646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 21580 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) : 0.6203063 object centre at (A) : 42.80950 28.05200 35.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0187601E-03 1.2294866E-02 midg,1,midg; midg,igrid,midg 6.7532854E-03 -1.7985603E-02 1,midg,midg; igrid,midg,midg -5.6642178E-02 2.3617448E-02 gauss-seidel spectral radius is 0.9986121 estimated iterations to convergence 213 setup time was (sec) 0.7400000 now iterating at: 15:03:14 rms-change max change #iterations 4.364808 184.7339 at 10iterations 2.020352 69.93863 at 20iterations 0.9386877 30.74372 at 30iterations 0.4348461 15.36661 at 40iterations 0.2024492 5.913129 at 50iterations 9.4018459E-02 3.041118 at 60iterations 4.3695331E-02 1.327176 at 70iterations 2.0264706E-02 0.6941605 at 80iterations 9.4439322E-03 0.2827483 at 90iterations 4.3973862E-03 0.1247702 at 100iterations 2.0489085E-03 6.1962128E-02 at 110iterations 9.5051969E-04 3.0027390E-02 at 120iterations finished qdiffx linear iterations at : 15:03:24 total time elapsed so far: 10.37000 # loops : 120 mean,max change (kT/e) : 9.5051969E-04 3.0027390E-02 energy calculations done at 10.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 15:03:24 10.503u 0.387s 0:11.17 97.4% 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 Sun Oct 16 2011 at 15:03:24 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2893 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.791378 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): 14.11400 71.50500 ymin,ymax (A): 4.319000 51.78500 zmin,zma (A): 7.626000 63.62800 x,y,z range (A): 57.39101 47.46600 56.00200 scale (grids/A): 2.791378 object centre (A): 42.80950 28.05200 35.62700 number of atom coordinates read : 2893 total number of charged atoms : 2752 net assigned charge : -1.985969 assigned positive charge : 436.4400 centred at (gu) : 85.60001 91.29555 93.97508 assigned negative charge : -438.4272 centred at (gu) : 85.32835 91.66756 94.15141 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 187151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27340 grid for indexing accessible points = 1.400000 m= 91990 mr = 132225 m= 32105 mr = 73763 m= 7513 mr = 25101 m= 1015 mr = 5498 m= 72 mr = 605 m= 0 mr = 31 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2111 time to turn everything in is 1.160000 number of dielectric boundary points 82623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 22015 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) : 1.860919 object centre at (A) : 42.80950 28.05200 35.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3398713 0.2298271 midg,1,midg; midg,igrid,midg 7.7692449E-02 -0.1773118 1,midg,midg; igrid,midg,midg -0.6487536 0.3767008 gauss-seidel spectral radius is 0.9992757 estimated iterations to convergence 293 setup time was (sec) 1.520000 now iterating at: 15:03:26 rms-change max change #iterations 10.53801 305.3566 at 10iterations 6.296560 173.6954 at 20iterations 3.716944 81.29279 at 30iterations 2.188094 47.84798 at 40iterations 1.279607 26.16747 at 50iterations 0.7493514 14.49452 at 60iterations 0.4358574 8.731172 at 70iterations 0.2533446 4.584572 at 80iterations 0.1470463 2.668639 at 90iterations 8.5260436E-02 1.508996 at 100iterations 4.9498722E-02 0.9606018 at 110iterations 2.8664090E-02 0.5421638 at 120iterations 1.6609389E-02 0.2991219 at 130iterations 9.6196113E-03 0.1817837 at 140iterations 5.5681202E-03 0.1076598 at 150iterations 3.2162231E-03 6.1668396E-02 at 160iterations 1.8575549E-03 3.4631252E-02 at 170iterations 1.0725936E-03 1.8220901E-02 at 180iterations finished qdiffx linear iterations at : 15:03:42 total time elapsed so far: 17.58000 # loops : 180 mean,max change (kT/e) : 1.0725936E-03 1.8220901E-02 energy calculations done at 17.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.71000 DelPhi exited at 15:03:42 17.714u 0.382s 0:18.39 98.3% 0+0k 0+0io 0pf+0w