Sat Oct 8 23:38:56 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 Sat Oct 8 2011 at 23:38:56 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2554 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: WAT 1 has a net charge of 0.4170 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: 0.6219645 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): 83.86500 141.1030 ymin,ymax (A): -106.9640 -63.93900 zmin,zma (A): 67.90900 122.9460 x,y,z range (A): 57.23800 43.02501 55.03700 scale (grids/A): 0.6219645 object centre (A): 112.4840 -85.45150 95.42750 number of atom coordinates read : 2554 total number of charged atoms : 2417 net assigned charge : 9.931032 assigned positive charge : 379.1029 centred at (gu) : 88.69991 89.67591 89.77821 assigned negative charge : -369.1728 centred at (gu) : 88.74313 89.77747 89.90578 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6768 nv = 96 ne = 84 npr = 50658 no. pairs analyzed = 50658 no. exposed pairs = 3363 no. arc points = 23439 no. surface atoms = 1127 nbur = 1427 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3587 m= 2 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7636111E-08 -2.2072581E-10 midg,1,midg; midg,igrid,midg 1.6212910E-08 1.4526644E-09 1,midg,midg; igrid,midg,midg 1.4939587E-08 4.2122061E-09 gauss-seidel spectral radius is 0.9866164 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 23:38:57 rms-change max change #iterations 0.1288213 17.67957 at 10iterations 1.1969312E-02 1.688712 at 20iterations 1.1937519E-03 0.1640301 at 30iterations 1.9509661E-04 3.2316208E-02 at 40iterations 4.9666505E-05 8.3608627E-03 at 50iterations finished qdiffx linear iterations at : 23:39:00 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 4.9666505E-05 8.3608627E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 23:39:00 3.718u 0.224s 0:04.43 88.7% 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 Sat Oct 8 2011 at 23:39:00 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2554 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: WAT 1 has a net charge of 0.4170 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: 1.865893 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): 83.86500 141.1030 ymin,ymax (A): -106.9640 -63.93900 zmin,zma (A): 67.90900 122.9460 x,y,z range (A): 57.23800 43.02501 55.03700 scale (grids/A): 1.865893 object centre (A): 112.4840 -85.45150 95.42750 number of atom coordinates read : 2554 total number of charged atoms : 2417 net assigned charge : 9.931032 assigned positive charge : 379.1029 centred at (gu) : 86.09931 89.02732 89.33424 assigned negative charge : -369.1728 centred at (gu) : 86.22927 89.33242 89.71748 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72316 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23439 grid for indexing accessible points = 1.400000 m= 27128 mr = 49087 m= 4562 mr = 19771 m= 239 mr = 2905 m= 0 mr = 60 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 32422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18986 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) : 0.6219645 object centre at (A) : 112.4840 -85.45150 95.42750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6274439E-02 -8.9012627E-03 midg,1,midg; midg,igrid,midg 2.2700900E-02 -7.3467509E-04 1,midg,midg; igrid,midg,midg 4.8125353E-02 5.1642157E-02 gauss-seidel spectral radius is 0.9985850 estimated iterations to convergence 211 setup time was (sec) 0.6100000 now iterating at: 23:39:01 rms-change max change #iterations 4.034081 172.5794 at 10iterations 1.861882 60.87828 at 20iterations 0.8577087 29.69527 at 30iterations 0.3979336 13.20398 at 40iterations 0.1835722 5.441863 at 50iterations 8.4743291E-02 3.110191 at 60iterations 3.9078236E-02 1.277622 at 70iterations 1.8228464E-02 0.6733398 at 80iterations 8.4084235E-03 0.2910995 at 90iterations 3.9264867E-03 0.1425995 at 100iterations 1.8474759E-03 5.9578896E-02 at 110iterations 8.8184682E-04 3.2241821E-02 at 120iterations finished qdiffx linear iterations at : 23:39:08 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 8.8184682E-04 3.2241821E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 23:39:09 7.721u 0.222s 0:08.42 94.2% 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 Sat Oct 8 2011 at 23:39:09 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2554 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: WAT 1 has a net charge of 0.4170 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: 2.798840 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): 83.86500 141.1030 ymin,ymax (A): -106.9640 -63.93900 zmin,zma (A): 67.90900 122.9460 x,y,z range (A): 57.23800 43.02501 55.03700 scale (grids/A): 2.798840 object centre (A): 112.4840 -85.45150 95.42750 number of atom coordinates read : 2554 total number of charged atoms : 2417 net assigned charge : 9.931032 assigned positive charge : 379.1029 centred at (gu) : 84.14883 88.54090 89.00108 assigned negative charge : -369.1728 centred at (gu) : 84.34396 88.99859 89.57619 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 166592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23439 grid for indexing accessible points = 1.400000 m= 85547 mr = 118703 m= 33074 mr = 69254 m= 8305 mr = 26626 m= 1099 mr = 6246 m= 59 mr = 718 m= 4 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 73109 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19324 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) : 1.865893 object centre at (A) : 112.4840 -85.45150 95.42750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4916453 -0.3321756 midg,1,midg; midg,igrid,midg 0.2351089 -4.6295717E-02 1,midg,midg; igrid,midg,midg 0.6577351 0.8034264 gauss-seidel spectral radius is 0.9992543 estimated iterations to convergence 289 setup time was (sec) 1.160000 now iterating at: 23:39:10 rms-change max change #iterations 9.649096 358.5915 at 10iterations 5.684126 138.5248 at 20iterations 3.314043 72.06496 at 30iterations 1.928114 42.47338 at 40iterations 1.115728 21.77378 at 50iterations 0.6448554 11.66720 at 60iterations 0.3707720 8.312800 at 70iterations 0.2140883 4.270325 at 80iterations 0.1230988 2.303792 at 90iterations 7.0795052E-02 1.393188 at 100iterations 4.0622648E-02 0.7679176 at 110iterations 2.3423163E-02 0.4287529 at 120iterations 1.3445110E-02 0.2436132 at 130iterations 7.7167824E-03 0.1520710 at 140iterations 4.4299550E-03 8.2183838E-02 at 150iterations 2.5431844E-03 4.6232224E-02 at 160iterations 1.4657606E-03 3.0460358E-02 at 170iterations 8.4765401E-04 1.5249252E-02 at 180iterations finished qdiffx linear iterations at : 23:39:22 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 8.4765401E-04 1.5249252E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 23:39:22 12.890u 0.235s 0:13.46 97.4% 0+0k 0+0io 0pf+0w