Mon Oct 10 19:34:15 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 Mon Oct 10 2011 at 19:34:15 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6227804 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): -8.849000 48.31400 ymin,ymax (A): -7.802000 38.45800 zmin,zma (A): 0.2670000 57.22300 x,y,z range (A): 57.16300 46.26000 56.95601 scale (grids/A): 0.6227804 object centre (A): 19.73250 15.32800 28.74500 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : -3.485968 assigned positive charge : 421.0092 centred at (gu) : 89.24671 89.52494 88.42828 assigned negative charge : -424.4962 centred at (gu) : 89.18314 89.40291 88.31500 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7173 nv = 96 ne = 84 npr = 55734 no. pairs analyzed = 55734 no. exposed pairs = 3735 no. arc points = 26308 no. surface atoms = 1252 nbur = 1531 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3660 m= 0 mr = 31 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3500000 number of dielectric boundary points 3856 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2635 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6727759E-08 4.1957806E-09 midg,1,midg; midg,igrid,midg -1.3874571E-08 5.9812515E-09 1,midg,midg; igrid,midg,midg -9.2120782E-09 1.8145042E-09 gauss-seidel spectral radius is 0.9866688 estimated iterations to convergence 71 setup time was (sec) 0.6900000 now iterating at: 19:34:16 rms-change max change #iterations 0.1321483 18.44815 at 10iterations 1.2412812E-02 1.706745 at 20iterations 1.1544627E-03 0.1745806 at 30iterations 1.0618712E-04 1.3442993E-02 at 40iterations 9.9621184E-06 1.4343262E-03 at 50iterations finished qdiffx linear iterations at : 19:34:21 total time elapsed so far: 5.640000 # loops : 50 mean,max change (kT/e) : 9.9621184E-06 1.4343262E-03 energy calculations done at 5.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.780000 DelPhi exited at 19:34:21 5.782u 0.464s 0:06.62 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 Mon Oct 10 2011 at 19:34:21 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.868341 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): -8.849000 48.31400 ymin,ymax (A): -7.802000 38.45800 zmin,zma (A): 0.2670000 57.22300 x,y,z range (A): 57.16300 46.26000 56.95601 scale (grids/A): 1.868341 object centre (A): 19.73250 15.32800 28.74500 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : -3.485968 assigned positive charge : 421.0092 centred at (gu) : 87.73924 88.57429 85.28391 assigned negative charge : -424.4962 centred at (gu) : 87.54902 88.20840 84.94471 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77698 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26308 grid for indexing accessible points = 1.400000 m= 26105 mr = 51912 m= 3628 mr = 18112 m= 178 mr = 1985 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 540 time to turn everything in is 0.6500000 number of dielectric boundary points 35560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 174 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20727 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) : 0.6227804 object centre at (A) : 19.73250 15.32800 28.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7082525E-02 2.0719619E-02 midg,1,midg; midg,igrid,midg -1.7119203E-02 5.0201677E-03 1,midg,midg; igrid,midg,midg -5.0303120E-02 2.5807360E-02 gauss-seidel spectral radius is 0.9986051 estimated iterations to convergence 212 setup time was (sec) 0.9900000 now iterating at: 19:34:23 rms-change max change #iterations 4.285164 172.8612 at 10iterations 1.981440 84.89697 at 20iterations 0.9174379 29.55928 at 30iterations 0.4250533 13.83724 at 40iterations 0.1971581 6.328190 at 50iterations 9.1443971E-02 2.805332 at 60iterations 4.2382605E-02 1.366093 at 70iterations 1.9691441E-02 0.5776749 at 80iterations 9.1509288E-03 0.2817011 at 90iterations 4.2314632E-03 0.1308594 at 100iterations 1.9655128E-03 6.3533783E-02 at 110iterations 9.1482286E-04 2.9648781E-02 at 120iterations finished qdiffx linear iterations at : 19:34:35 total time elapsed so far: 12.76000 # loops : 120 mean,max change (kT/e) : 9.1482286E-04 2.9648781E-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) 12.93000 DelPhi exited at 19:34:35 12.937u 0.535s 0:13.78 97.6% 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 19:34:35 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2783 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.802512 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): -8.849000 48.31400 ymin,ymax (A): -7.802000 38.45800 zmin,zma (A): 0.2670000 57.22300 x,y,z range (A): 57.16300 46.26000 56.95601 scale (grids/A): 2.802512 object centre (A): 19.73250 15.32800 28.74500 number of atom coordinates read : 2783 total number of charged atoms : 2643 net assigned charge : -3.485968 assigned positive charge : 421.0092 centred at (gu) : 86.60869 87.86131 82.92596 assigned negative charge : -424.4962 centred at (gu) : 86.32345 87.31262 82.41689 start vw surface at 0.1300000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 179713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26308 grid for indexing accessible points = 1.400000 m= 85919 mr = 126723 m= 28918 mr = 67863 m= 6128 mr = 22099 m= 696 mr = 4194 m= 35 mr = 375 m= 0 mr = 4 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1620 time to turn everything in is 1.680000 number of dielectric boundary points 80151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 21144 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) : 1.868341 object centre at (A) : 19.73250 15.32800 28.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1617027 0.3883517 midg,1,midg; midg,igrid,midg -0.1368900 4.9488377E-02 1,midg,midg; igrid,midg,midg -0.6967362 0.3597214 gauss-seidel spectral radius is 0.9992718 estimated iterations to convergence 292 setup time was (sec) 2.080000 now iterating at: 19:34:38 rms-change max change #iterations 10.42944 378.4241 at 10iterations 6.209282 169.7141 at 20iterations 3.652518 91.61043 at 30iterations 2.143606 54.69085 at 40iterations 1.249666 28.60331 at 50iterations 0.7281759 14.00713 at 60iterations 0.4228754 9.603315 at 70iterations 0.2452246 4.718335 at 80iterations 0.1424768 2.550728 at 90iterations 8.2316294E-02 1.887064 at 100iterations 4.7681104E-02 0.9111214 at 110iterations 2.7515646E-02 0.5330868 at 120iterations 1.5909687E-02 0.3093014 at 130iterations 9.1956193E-03 0.1689255 at 140iterations 5.3036325E-03 9.7442627E-02 at 150iterations 3.0584328E-03 5.6612015E-02 at 160iterations 1.7645247E-03 3.0986786E-02 at 170iterations 1.0190211E-03 1.8769979E-02 at 180iterations finished qdiffx linear iterations at : 19:34:58 total time elapsed so far: 22.74000 # loops : 180 mean,max change (kT/e) : 1.0190211E-03 1.8769979E-02 energy calculations done at 22.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.91000 DelPhi exited at 19:34:59 22.913u 0.526s 0:23.99 97.6% 0+0k 0+0io 0pf+0w