Wed Dec 21 14:22:38 PST 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 Wed Dec 21 2011 at 14:22:40 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ASN 136 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6349432 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): -4.650000 35.63700 ymin,ymax (A): -4.342000 49.00400 zmin,zma (A): -24.45300 31.61500 x,y,z range (A): 40.28700 53.34600 56.06800 scale (grids/A): 0.6349432 object centre (A): 15.49350 22.33100 3.581000 number of atom coordinates read : 1970 total number of charged atoms : 1766 net assigned charge : -23.32802 assigned positive charge : 267.6724 centred at (gu) : 90.26200 92.26405 89.95077 assigned negative charge : -291.0002 centred at (gu) : 90.35447 92.38940 89.90651 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5386 nv = 96 ne = 84 npr = 40428 no. pairs analyzed = 40428 no. exposed pairs = 2440 no. arc points = 17153 no. surface atoms = 829 nbur = 1141 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 267 mr = 3009 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3100000 number of dielectric boundary points 2611 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1607 ## 110 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 6216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2598535E-08 -2.5310916E-08 midg,1,midg; midg,igrid,midg -1.2435976E-08 -6.2503283E-08 1,midg,midg; igrid,midg,midg -2.0834118E-08 -3.8006071E-08 gauss-seidel spectral radius is 0.9870944 estimated iterations to convergence 72 setup time was (sec) 0.7800000 now iterating at: 14:22:42 rms-change max change #iterations 0.1303511 21.08167 at 10iterations 1.2472567E-02 2.252617 at 20iterations 1.2064154E-03 0.1903191 at 30iterations 1.1820283E-04 1.9252539E-02 at 40iterations 1.1232882E-05 2.0275116E-03 at 50iterations finished qdiffx linear iterations at : 14:22:49 total time elapsed so far: 7.750000 # loops : 50 mean,max change (kT/e) : 1.1232882E-05 2.0275116E-03 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.920000 DelPhi exited at 14:22:55 7.927u 0.701s 0:15.13 56.9% 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 Wed Dec 21 2011 at 14:22:57 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ASN 136 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.904830 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): -4.650000 35.63700 ymin,ymax (A): -4.342000 49.00400 zmin,zma (A): -24.45300 31.61500 x,y,z range (A): 40.28700 53.34600 56.06800 scale (grids/A): 1.904830 object centre (A): 15.49350 22.33100 3.581000 number of atom coordinates read : 1970 total number of charged atoms : 1766 net assigned charge : -23.32802 assigned positive charge : 267.6724 centred at (gu) : 90.78639 96.79234 89.85259 assigned negative charge : -291.0002 centred at (gu) : 91.06345 97.16840 89.71970 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 58528 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17153 grid for indexing accessible points = 1.400000 m= 21467 mr = 40658 m= 2962 mr = 16509 m= 163 mr = 1842 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1170 time to turn everything in is 0.4900000 number of dielectric boundary points 24058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13902 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) : 0.6349432 object centre at (A) : 15.49350 22.33100 3.581000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9232953E-04 -7.1369432E-02 midg,1,midg; midg,igrid,midg -1.4068213E-02 -8.2184553E-02 1,midg,midg; igrid,midg,midg -1.4454780E-02 -4.0958550E-02 gauss-seidel spectral radius is 0.9985575 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 14:22:59 rms-change max change #iterations 3.635148 167.2630 at 10iterations 1.660995 61.10524 at 20iterations 0.7618276 30.60614 at 30iterations 0.3502199 12.31244 at 40iterations 0.1603090 5.764273 at 50iterations 7.3552079E-02 2.669342 at 60iterations 3.3714984E-02 1.125343 at 70iterations 1.5414183E-02 0.5638275 at 80iterations 7.0863925E-03 0.2460957 at 90iterations 3.2352908E-03 0.1165085 at 100iterations 1.4913175E-03 5.9219360E-02 at 110iterations 6.8186235E-04 2.3681641E-02 at 120iterations finished qdiffx linear iterations at : 14:23:13 total time elapsed so far: 14.02000 # loops : 120 mean,max change (kT/e) : 6.8186235E-04 2.3681641E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.19000 DelPhi exited at 14:23:15 14.195u 0.464s 0:18.12 80.8% 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 Wed Dec 21 2011 at 14:23:15 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ASN 37 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ASN 136 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.857245 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): -4.650000 35.63700 ymin,ymax (A): -4.342000 49.00400 zmin,zma (A): -24.45300 31.61500 x,y,z range (A): 40.28700 53.34600 56.06800 scale (grids/A): 2.857245 object centre (A): 15.49350 22.33100 3.581000 number of atom coordinates read : 1970 total number of charged atoms : 1766 net assigned charge : -23.32802 assigned positive charge : 267.6724 centred at (gu) : 91.17966 100.1886 89.77902 assigned negative charge : -291.0002 centred at (gu) : 91.59526 100.7526 89.57954 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 135241 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17153 grid for indexing accessible points = 1.400000 m= 69802 mr = 98154 m= 24872 mr = 58356 m= 5080 mr = 20554 m= 634 mr = 3844 m= 38 mr = 439 m= 0 mr = 17 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 3795 time to turn everything in is 1.480000 number of dielectric boundary points 54303 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 14128 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) : 1.904830 object centre at (A) : 15.49350 22.33100 3.581000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7785345 -0.7660540 midg,1,midg; midg,igrid,midg -1.5641257E-02 -0.8722787 1,midg,midg; igrid,midg,midg -0.1301564 -0.4042175 gauss-seidel spectral radius is 0.9992223 estimated iterations to convergence 283 setup time was (sec) 2.050000 now iterating at: 14:23:18 rms-change max change #iterations 8.423459 402.3105 at 10iterations 4.804901 117.5481 at 20iterations 2.709269 60.17824 at 30iterations 1.531703 32.30897 at 40iterations 0.8664674 17.29626 at 50iterations 0.4899964 9.268375 at 60iterations 0.2762758 6.093147 at 70iterations 0.1565151 3.184474 at 80iterations 8.8454403E-02 1.724804 at 90iterations 4.9985196E-02 1.092239 at 100iterations 2.8209405E-02 0.5442910 at 110iterations 1.5934009E-02 0.3148446 at 120iterations 9.0079922E-03 0.1778889 at 130iterations 5.0851395E-03 0.1029778 at 140iterations 2.8732896E-03 5.5297852E-02 at 150iterations 1.6262188E-03 3.5888672E-02 at 160iterations 9.1891328E-04 2.0030022E-02 at 170iterations 5.1966199E-04 1.0704041E-02 at 180iterations finished qdiffx linear iterations at : 14:23:45 total time elapsed so far: 29.42000 # loops : 180 mean,max change (kT/e) : 5.1966199E-04 1.0704041E-02 energy calculations done at 29.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.59000 DelPhi exited at 14:23:46 29.592u 0.823s 0:30.78 98.7% 0+0k 0+0io 0pf+0w