Wed Dec 28 11:01:59 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 11:01:59 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5825751 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): -25.62800 35.48000 ymin,ymax (A): -19.02600 20.67700 zmin,zma (A): -3.370000 38.56400 x,y,z range (A): 61.10800 39.70300 41.93400 scale (grids/A): 0.5825751 object centre (A): 4.926002 0.8255005 17.59700 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.97689 90.25674 90.52785 assigned negative charge : -285.8263 centred at (gu) : 89.98035 90.35709 90.67873 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4480 nv = 96 ne = 84 npr = 40422 no. pairs analyzed = 40422 no. exposed pairs = 2408 no. arc points = 17114 no. surface atoms = 821 nbur = 1143 mkacc time = 0.1300000 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 = 1.484000 m= 202 mr = 2433 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.3100000 number of dielectric boundary points 2237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1719 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 5436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6231797E-09 -8.5738616E-09 midg,1,midg; midg,igrid,midg -3.4927519E-09 -7.2010615E-09 1,midg,midg; igrid,midg,midg -5.1986020E-09 -5.2506248E-09 gauss-seidel spectral radius is 0.9847069 estimated iterations to convergence 66 setup time was (sec) 0.7800000 now iterating at: 11:02:01 rms-change max change #iterations 8.1809409E-02 16.56666 at 10iterations 6.3966569E-03 1.173401 at 20iterations 5.1399943E-04 9.9441528E-02 at 30iterations 3.8993232E-05 6.7138672E-03 at 40iterations 3.1393556E-06 5.0163269E-04 at 50iterations finished qdiffx linear iterations at : 11:02:07 total time elapsed so far: 7.000000 # loops : 50 mean,max change (kT/e) : 3.1393556E-06 5.0163269E-04 energy calculations done at 7.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 11:02:09 7.226u 0.590s 0:09.54 81.8% 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 11:02:09 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.747725 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): -25.62800 35.48000 ymin,ymax (A): -19.02600 20.67700 zmin,zma (A): -3.370000 38.56400 x,y,z range (A): 61.10800 39.70300 41.93400 scale (grids/A): 1.747725 object centre (A): 4.926002 0.8255005 17.59700 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.93114 90.77052 91.58390 assigned negative charge : -285.8263 centred at (gu) : 89.94112 91.07144 92.03632 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 48823 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17114 grid for indexing accessible points = 1.400000 m= 16603 mr = 33353 m= 1914 mr = 12411 m= 52 mr = 1080 m= 0 mr = 10 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 0.5100000 number of dielectric boundary points 20538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13753 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) : 0.5825751 object centre at (A) : 4.926002 0.8255005 17.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9220328E-03 -2.7147911E-02 midg,1,midg; midg,igrid,midg -1.1481065E-02 -2.2594210E-02 1,midg,midg; igrid,midg,midg -2.6962062E-02 -3.2669857E-02 gauss-seidel spectral radius is 0.9983022 estimated iterations to convergence 193 setup time was (sec) 0.8600000 now iterating at: 11:02:10 rms-change max change #iterations 2.993169 158.8936 at 10iterations 1.280383 59.14737 at 20iterations 0.5497963 25.80723 at 30iterations 0.2353572 9.963905 at 40iterations 0.1012100 4.715446 at 50iterations 4.3318335E-02 1.812291 at 60iterations 1.8612690E-02 0.7842159 at 70iterations 7.9410616E-03 0.3146896 at 80iterations 3.4226649E-03 0.1531518 at 90iterations 1.4607736E-03 6.2994003E-02 at 100iterations 6.2780030E-04 2.5987148E-02 at 110iterations 2.7018305E-04 1.1257172E-02 at 120iterations finished qdiffx linear iterations at : 11:02:25 total time elapsed so far: 15.93000 # loops : 120 mean,max change (kT/e) : 2.7018305E-04 1.1257172E-02 energy calculations done at 15.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.16000 DelPhi exited at 11:02:27 16.162u 0.499s 0:17.92 92.9% 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 28 2011 at 11:02:27 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.621588 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): -25.62800 35.48000 ymin,ymax (A): -19.02600 20.67700 zmin,zma (A): -3.370000 38.56400 x,y,z range (A): 61.10800 39.70300 41.93400 scale (grids/A): 2.621588 object centre (A): 4.926002 0.8255005 17.59700 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.89687 91.15591 92.37603 assigned negative charge : -285.8263 centred at (gu) : 89.91185 91.60714 93.05458 start vw surface at 0.1400000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 112959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17114 grid for indexing accessible points = 1.400000 m= 56026 mr = 80985 m= 17715 mr = 46167 m= 3061 mr = 14302 m= 238 mr = 2164 m= 11 mr = 134 m= 0 mr = 3 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 6558 time to turn everything in is 1.400000 number of dielectric boundary points 46255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 14105 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) : 1.747725 object centre at (A) : 4.926002 0.8255005 17.59700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5717312E-02 -0.3182271 midg,1,midg; midg,igrid,midg -0.1305170 -0.2668089 1,midg,midg; igrid,midg,midg -0.3268987 -0.4278287 gauss-seidel spectral radius is 0.9991432 estimated iterations to convergence 270 setup time was (sec) 1.760000 now iterating at: 11:02:29 rms-change max change #iterations 7.289615 309.9007 at 10iterations 4.053791 106.6057 at 20iterations 2.240360 58.39917 at 30iterations 1.234271 28.98316 at 40iterations 0.6795583 15.34530 at 50iterations 0.3730419 9.036049 at 60iterations 0.2049068 4.534874 at 70iterations 0.1126819 2.475723 at 80iterations 6.1808646E-02 1.477198 at 90iterations 3.4002624E-02 0.8160839 at 100iterations 1.8680783E-02 0.4517403 at 110iterations 1.0227850E-02 0.2397251 at 120iterations 5.6179152E-03 0.1432114 at 130iterations 3.0941155E-03 7.3976517E-02 at 140iterations 1.6990276E-03 3.9140701E-02 at 150iterations 9.3216891E-04 2.1453857E-02 at 160iterations 5.1184866E-04 1.1362076E-02 at 170iterations 2.8166384E-04 6.4258575E-03 at 180iterations finished qdiffx linear iterations at : 11:02:54 total time elapsed so far: 26.51000 # loops : 180 mean,max change (kT/e) : 2.8166384E-04 6.4258575E-03 energy calculations done at 26.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 26.74000 DelPhi exited at 11:02:55 26.744u 0.534s 0:27.90 97.7% 0+0k 0+0io 0pf+0w