Sun Oct 9 07:02:30 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 07:02:30 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 0.6957746 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): -24.19900 25.29900 ymin,ymax (A): 0.7770001 45.61900 zmin,zma (A): -23.69000 27.47600 x,y,z range (A): 49.49800 44.84200 51.16600 scale (grids/A): 0.6957746 object centre (A): 0.5499992 23.19800 1.893000 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 89.32976 89.66028 89.35859 assigned negative charge : -302.1561 centred at (gu) : 89.26184 89.86868 89.33699 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6493 nv = 96 ne = 84 npr = 42370 no. pairs analyzed = 42370 no. exposed pairs = 2496 no. arc points = 17277 no. surface atoms = 842 nbur = 1159 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3611 m= 0 mr = 48 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2900000 number of dielectric boundary points 3191 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1567 ## 126 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7352 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7010133E-08 -7.0972583E-09 midg,1,midg; midg,igrid,midg 6.3373349E-08 -8.7878782E-08 1,midg,midg; igrid,midg,midg -4.6845777E-08 7.6678912E-09 gauss-seidel spectral radius is 0.9892309 estimated iterations to convergence 78 setup time was (sec) 0.5600000 now iterating at: 07:02:31 rms-change max change #iterations 0.1839030 28.37834 at 10iterations 2.2405479E-02 3.101728 at 20iterations 2.6157366E-03 0.3805428 at 30iterations 3.1202292E-04 4.5135498E-02 at 40iterations 3.6864385E-05 5.3520203E-03 at 50iterations finished qdiffx linear iterations at : 07:02:34 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 3.6864385E-05 5.3520203E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 07:02:35 4.002u 0.272s 0:04.54 94.0% 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 Sun Oct 9 2011 at 07:02:35 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 2.087324 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): -24.19900 25.29900 ymin,ymax (A): 0.7770001 45.61900 zmin,zma (A): -23.69000 27.47600 x,y,z range (A): 49.49800 44.84200 51.16600 scale (grids/A): 2.087324 object centre (A): 0.5499992 23.19800 1.893000 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 87.98949 88.98090 88.07562 assigned negative charge : -302.1561 centred at (gu) : 87.78559 89.60622 88.01099 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69564 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17277 grid for indexing accessible points = 1.400000 m= 25650 mr = 48279 m= 4395 mr = 19187 m= 340 mr = 2902 m= 7 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1214 time to turn everything in is 0.6400000 number of dielectric boundary points 29425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14770 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) : 0.6957746 object centre at (A) : 0.5499992 23.19800 1.893000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1769191E-02 8.3019333E-03 midg,1,midg; midg,igrid,midg 6.6607483E-02 -4.8363112E-02 1,midg,midg; igrid,midg,midg -5.4637678E-02 -1.1490718E-02 gauss-seidel spectral radius is 0.9987919 estimated iterations to convergence 228 setup time was (sec) 0.9300000 now iterating at: 07:02:36 rms-change max change #iterations 4.468671 200.2114 at 10iterations 2.179079 82.89075 at 20iterations 1.066334 38.00462 at 30iterations 0.5218717 18.18199 at 40iterations 0.2553547 8.909208 at 50iterations 0.1252540 4.034184 at 60iterations 6.1408021E-02 1.781907 at 70iterations 3.0119350E-02 0.9836860 at 80iterations 1.4663032E-02 0.4129906 at 90iterations 7.2291582E-03 0.2386230 at 100iterations 3.5338127E-03 0.1089392 at 110iterations 1.7240698E-03 5.2664757E-02 at 120iterations finished qdiffx linear iterations at : 07:02:44 total time elapsed so far: 9.180000 # loops : 120 mean,max change (kT/e) : 1.7240698E-03 5.2664757E-02 energy calculations done at 9.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 07:02:45 9.364u 0.287s 0:09.92 97.1% 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 07:02:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 188 has a net charge of -3.0000 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: 3.130985 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): -24.19900 25.29900 ymin,ymax (A): 0.7770001 45.61900 zmin,zma (A): -23.69000 27.47600 x,y,z range (A): 49.49800 44.84200 51.16600 scale (grids/A): 3.130985 object centre (A): 0.5499992 23.19800 1.893000 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499985 assigned positive charge : 299.6560 centred at (gu) : 86.98421 88.47125 87.11346 assigned negative charge : -302.1561 centred at (gu) : 86.67832 89.40929 87.01642 start vw surface at 0.1400000 fill in re-entrant regions at 0.9300000 boundary points on vw surface= 160740 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17277 grid for indexing accessible points = 1.400000 m= 81834 mr = 116518 m= 30694 mr = 67675 m= 8157 mr = 25023 m= 1429 mr = 6322 m= 134 mr = 986 m= 6 mr = 84 m= 0 mr = 4 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 4085 time to turn everything in is 2.010000 number of dielectric boundary points 66382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 14896 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) : 2.087324 object centre at (A) : 0.5499992 23.19800 1.893000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7908944 0.5263556 midg,1,midg; midg,igrid,midg 0.7810202 -0.5228177 1,midg,midg; igrid,midg,midg -0.4859595 -0.1139258 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 2.350000 now iterating at: 07:02:47 rms-change max change #iterations 10.02123 357.9026 at 10iterations 5.826519 119.8509 at 20iterations 3.384870 74.35622 at 30iterations 1.970019 39.38552 at 40iterations 1.144129 21.34614 at 50iterations 0.6626402 11.98758 at 60iterations 0.3843738 7.139793 at 70iterations 0.2230306 3.821388 at 80iterations 0.1293267 2.406820 at 90iterations 7.5074747E-02 1.420827 at 100iterations 4.3427967E-02 0.7102845 at 110iterations 2.5183113E-02 0.4523277 at 120iterations 1.4586355E-02 0.2587967 at 130iterations 8.4831575E-03 0.1587067 at 140iterations 4.9065575E-03 8.2829475E-02 at 150iterations 2.8460077E-03 5.8288574E-02 at 160iterations 1.6505355E-03 3.1351089E-02 at 170iterations 9.5789100E-04 1.6988754E-02 at 180iterations finished qdiffx linear iterations at : 07:03:02 total time elapsed so far: 17.48000 # loops : 180 mean,max change (kT/e) : 9.5789100E-04 1.6988754E-02 energy calculations done at 17.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.65000 DelPhi exited at 07:03:03 17.656u 0.309s 0:18.24 98.4% 0+0k 0+0io 0pf+0w