Wed Dec 28 11:01:17 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+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 Wed Dec 28 2011 at 11:01:17 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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: 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: 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5703391 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): -34.86100 9.945001 ymin,ymax (A): 0.7150000 40.87400 zmin,zma (A): -2.459000 59.96000 x,y,z range (A): 44.80600 40.15900 62.41900 scale (grids/A): 0.5703391 object centre (A): -12.45800 20.79450 28.75050 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 263.6024 centred at (gu) : 90.41727 89.73124 89.49960 assigned negative charge : -285.5543 centred at (gu) : 90.31699 89.86727 89.53162 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4253 nv = 96 ne = 84 npr = 40154 no. pairs analyzed = 40154 no. exposed pairs = 2445 no. arc points = 17098 no. surface atoms = 836 nbur = 1122 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 175 mr = 2265 m= 0 mr = 11 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1645 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5213 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4691920E-09 -3.3379557E-09 midg,1,midg; midg,igrid,midg -2.1776108E-09 -4.5372821E-09 1,midg,midg; igrid,midg,midg -4.0432280E-09 -2.6438658E-09 gauss-seidel spectral radius is 0.9840524 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 11:01:18 rms-change max change #iterations 7.5318351E-02 14.06648 at 10iterations 5.4991720E-03 1.015593 at 20iterations 4.2415340E-04 6.9427490E-02 at 30iterations 3.1408195E-05 5.7563782E-03 at 40iterations 2.3856810E-06 4.1937828E-04 at 50iterations finished qdiffx linear iterations at : 11:01:22 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.3856810E-06 4.1937828E-04 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.570000 DelPhi exited at 11:01:23 4.579u 0.393s 0:05.75 86.2% 0+0k 0+0io 6pf+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 28 2011 at 11:01:23 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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: 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: 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.711017 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): -34.86100 9.945001 ymin,ymax (A): 0.7150000 40.87400 zmin,zma (A): -2.459000 59.96000 x,y,z range (A): 44.80600 40.15900 62.41900 scale (grids/A): 1.711017 object centre (A): -12.45800 20.79450 28.75050 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 263.6024 centred at (gu) : 91.25193 89.19392 88.49882 assigned negative charge : -285.5543 centred at (gu) : 90.95110 89.60221 88.59486 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 46127 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17098 grid for indexing accessible points = 1.400000 m= 15201 mr = 31354 m= 1658 mr = 11005 m= 51 mr = 829 m= 2 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 19849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 130 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 13666 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) : 0.5703391 object centre at (A) : -12.45800 20.79450 28.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9176757E-02 -2.9554732E-02 midg,1,midg; midg,igrid,midg -1.0789393E-02 -2.3184152E-02 1,midg,midg; igrid,midg,midg -1.3209468E-02 -1.6136855E-02 gauss-seidel spectral radius is 0.9982274 estimated iterations to convergence 189 setup time was (sec) 0.7100000 now iterating at: 11:01:24 rms-change max change #iterations 2.869520 160.9486 at 10iterations 1.198549 52.10897 at 20iterations 0.5048571 24.17919 at 30iterations 0.2126381 8.966900 at 40iterations 8.9907788E-02 3.949287 at 50iterations 3.7732430E-02 1.663601 at 60iterations 1.5890390E-02 0.6311665 at 70iterations 6.6650738E-03 0.2694839 at 80iterations 2.8105795E-03 0.1177287 at 90iterations 1.1859788E-03 4.8326492E-02 at 100iterations 4.9883005E-04 2.0277023E-02 at 110iterations 2.1029635E-04 9.4919205E-03 at 120iterations finished qdiffx linear iterations at : 11:01:34 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 2.1029635E-04 9.4919205E-03 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 11:01:35 10.599u 0.445s 0:11.41 96.6% 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 Wed Dec 28 2011 at 11:01:35 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! 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: 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: 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: 2.566526 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): -34.86100 9.945001 ymin,ymax (A): 0.7150000 40.87400 zmin,zma (A): -2.459000 59.96000 x,y,z range (A): 44.80600 40.15900 62.41900 scale (grids/A): 2.566526 object centre (A): -12.45800 20.79450 28.75050 number of atom coordinates read : 1958 total number of charged atoms : 1758 net assigned charge : -21.95202 assigned positive charge : 263.6024 centred at (gu) : 91.87792 88.79095 87.74840 assigned negative charge : -285.5543 centred at (gu) : 91.42662 89.40323 87.89236 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 106613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17098 grid for indexing accessible points = 1.400000 m= 51428 mr = 76016 m= 15831 mr = 41660 m= 2599 mr = 12411 m= 231 mr = 1659 m= 5 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 44840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 14054 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) : 1.711017 object centre at (A) : -12.45800 20.79450 28.75050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5074082 -0.4653078 midg,1,midg; midg,igrid,midg -0.1312338 -0.3129971 1,midg,midg; igrid,midg,midg -0.1692130 -0.2246722 gauss-seidel spectral radius is 0.9991155 estimated iterations to convergence 266 setup time was (sec) 1.270000 now iterating at: 11:01:36 rms-change max change #iterations 7.114351 268.8176 at 10iterations 3.945300 110.9348 at 20iterations 2.178477 63.61078 at 30iterations 1.197025 31.25261 at 40iterations 0.6546422 17.86166 at 50iterations 0.3592483 8.461584 at 60iterations 0.1964414 5.046270 at 70iterations 0.1072833 2.735380 at 80iterations 5.8620725E-02 1.351694 at 90iterations 3.1851221E-02 0.7273579 at 100iterations 1.7400762E-02 0.4976101 at 110iterations 9.4616935E-03 0.2293110 at 120iterations 5.1682140E-03 0.1173973 at 130iterations 2.8147260E-03 6.8069458E-02 at 140iterations 1.5283372E-03 3.6118835E-02 at 150iterations 8.3435205E-04 2.0290375E-02 at 160iterations 4.5362848E-04 1.1450529E-02 at 170iterations 2.4693180E-04 6.2751770E-03 at 180iterations finished qdiffx linear iterations at : 11:01:52 total time elapsed so far: 17.14000 # loops : 180 mean,max change (kT/e) : 2.4693180E-04 6.2751770E-03 energy calculations done at 17.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.31000 DelPhi exited at 11:01:53 17.312u 0.458s 0:18.36 96.7% 0+0k 0+0io 0pf+0w