Sun Oct 9 06:33:12 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 Sun Oct 9 2011 at 06:33:12 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7021696 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): -22.00000 23.64200 ymin,ymax (A): 14.26400 59.05300 zmin,zma (A): -20.70100 29.99900 x,y,z range (A): 45.64200 44.78900 50.70000 scale (grids/A): 0.7021696 object centre (A): 0.8210001 36.65850 4.649000 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000144 assigned positive charge : 287.9030 centred at (gu) : 89.74538 89.19642 90.57896 assigned negative charge : -287.4032 centred at (gu) : 89.81689 89.40269 90.45939 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6555 nv = 96 ne = 84 npr = 40004 no. pairs analyzed = 40004 no. exposed pairs = 2498 no. arc points = 17874 no. surface atoms = 840 nbur = 1106 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3550 m= 4 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.1600000 number of dielectric boundary points 3350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1672 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 7245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1162803E-08 5.6735814E-08 midg,1,midg; midg,igrid,midg 9.9289998E-08 -7.0203654E-08 1,midg,midg; igrid,midg,midg 3.3070712E-08 -2.5101567E-08 gauss-seidel spectral radius is 0.9894246 estimated iterations to convergence 79 setup time was (sec) 0.3500000 now iterating at: 06:33:12 rms-change max change #iterations 0.1808897 30.39546 at 10iterations 2.1916082E-02 3.079502 at 20iterations 2.6626855E-03 0.4339237 at 30iterations 3.2099898E-04 4.5064926E-02 at 40iterations 3.8730133E-05 5.7945251E-03 at 50iterations finished qdiffx linear iterations at : 06:33:15 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 3.8730133E-05 5.7945251E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 06:33:16 3.323u 0.174s 0:03.84 90.8% 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 9 2011 at 06:33:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.106509 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): -22.00000 23.64200 ymin,ymax (A): 14.26400 59.05300 zmin,zma (A): -20.70100 29.99900 x,y,z range (A): 45.64200 44.78900 50.70000 scale (grids/A): 2.106509 object centre (A): 0.8210001 36.65850 4.649000 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000144 assigned positive charge : 287.9030 centred at (gu) : 89.23607 87.58913 91.73695 assigned negative charge : -287.4032 centred at (gu) : 89.45094 88.20813 91.37811 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 68954 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17874 grid for indexing accessible points = 1.400000 m= 26778 mr = 46633 m= 5267 mr = 20282 m= 488 mr = 3594 m= 8 mr = 242 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 845 time to turn everything in is 0.3400000 number of dielectric boundary points 30744 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14348 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) : 0.7021696 object centre at (A) : 0.8210001 36.65850 4.649000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0333179E-02 -1.4715302E-02 midg,1,midg; midg,igrid,midg 7.2080046E-02 -3.8462296E-02 1,midg,midg; igrid,midg,midg 1.4884262E-02 -9.7638303E-03 gauss-seidel spectral radius is 0.9988146 estimated iterations to convergence 230 setup time was (sec) 0.5500000 now iterating at: 06:33:16 rms-change max change #iterations 4.337923 194.0845 at 10iterations 2.115185 77.02316 at 20iterations 1.044173 34.20544 at 30iterations 0.5156330 16.27090 at 40iterations 0.2530060 7.875615 at 50iterations 0.1248870 4.229591 at 60iterations 6.1478909E-02 2.133243 at 70iterations 3.0331248E-02 0.9929752 at 80iterations 1.4905295E-02 0.4515991 at 90iterations 7.3393676E-03 0.2230873 at 100iterations 3.6244350E-03 0.1166916 at 110iterations 1.7863009E-03 5.5601120E-02 at 120iterations finished qdiffx linear iterations at : 06:33:23 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 1.7863009E-03 5.5601120E-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) 7.700000 DelPhi exited at 06:33:24 7.699u 0.211s 0:08.20 96.3% 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 Sun Oct 9 2011 at 06:33:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ASP 186 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.159763 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): -22.00000 23.64200 ymin,ymax (A): 14.26400 59.05300 zmin,zma (A): -20.70100 29.99900 x,y,z range (A): 45.64200 44.78900 50.70000 scale (grids/A): 3.159763 object centre (A): 0.8210001 36.65850 4.649000 number of atom coordinates read : 1946 total number of charged atoms : 1807 net assigned charge : 0.5000144 assigned positive charge : 287.9030 centred at (gu) : 88.85416 86.38366 92.60544 assigned negative charge : -287.4032 centred at (gu) : 89.17633 87.31223 92.06709 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 158737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17874 grid for indexing accessible points = 1.400000 m= 82611 mr = 112459 m= 34435 mr = 68117 m= 10093 mr = 28720 m= 1962 mr = 7923 m= 253 mr = 1457 m= 5 mr = 163 m= 0 mr = 2 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 2823 time to turn everything in is 1.040000 number of dielectric boundary points 69255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 14456 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) : 2.106509 object centre at (A) : 0.8210001 36.65850 4.649000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9573847E-02 -0.2362567 midg,1,midg; midg,igrid,midg 0.7384843 -0.2757182 1,midg,midg; igrid,midg,midg 0.1919797 -7.2942346E-02 gauss-seidel spectral radius is 0.9992953 estimated iterations to convergence 297 setup time was (sec) 1.270000 now iterating at: 06:33:25 rms-change max change #iterations 9.784527 451.6463 at 10iterations 5.729979 120.9041 at 20iterations 3.336840 62.29513 at 30iterations 1.949213 33.46452 at 40iterations 1.135832 20.21024 at 50iterations 0.6608728 13.17667 at 60iterations 0.3853261 8.135013 at 70iterations 0.2241791 3.816589 at 80iterations 0.1300839 2.390842 at 90iterations 7.5798653E-02 1.412508 at 100iterations 4.4096999E-02 0.8146496 at 110iterations 2.5579609E-02 0.4504204 at 120iterations 1.4872307E-02 0.2525299 at 130iterations 8.6484412E-03 0.1576538 at 140iterations 5.0320411E-03 8.8926792E-02 at 150iterations 2.9266586E-03 5.9695721E-02 at 160iterations 1.7032641E-03 2.9109955E-02 at 170iterations 9.8925817E-04 1.7623901E-02 at 180iterations finished qdiffx linear iterations at : 06:33:37 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 9.8925817E-04 1.7623901E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 06:33:37 12.662u 0.217s 0:13.16 97.7% 0+0k 0+0io 0pf+0w