Wed Dec 21 14:21:43 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 14:21:44 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: 263 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5790878 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): -25.77600 35.70000 ymin,ymax (A): -19.00900 20.62200 zmin,zma (A): -3.804000 38.55500 x,y,z range (A): 61.47600 39.63100 42.35900 scale (grids/A): 0.5790878 object centre (A): 4.962001 0.8065004 17.37550 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 89.97330 90.25732 90.64704 assigned negative charge : -289.0263 centred at (gu) : 89.97504 90.35348 90.79881 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4427 nv = 96 ne = 84 npr = 40136 no. pairs analyzed = 40136 no. exposed pairs = 2420 no. arc points = 17312 no. surface atoms = 816 nbur = 1148 mkacc time = 7.0000008E-02 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= 177 mr = 2389 m= 0 mr = 8 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.1600000 number of dielectric boundary points 2207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1691 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 5375 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2212412E-09 -7.8671647E-09 midg,1,midg; midg,igrid,midg -3.1220460E-09 -6.3407937E-09 1,midg,midg; igrid,midg,midg -4.6295399E-09 -4.6215787E-09 gauss-seidel spectral radius is 0.9845260 estimated iterations to convergence 66 setup time was (sec) 0.5300000 now iterating at: 14:21:45 rms-change max change #iterations 8.0357954E-02 13.50067 at 10iterations 6.5141022E-03 1.438862 at 20iterations 5.0061510E-04 0.1046791 at 30iterations 3.9023111E-05 6.5093040E-03 at 40iterations 2.9327857E-06 4.7969818E-04 at 50iterations finished qdiffx linear iterations at : 14:21:49 total time elapsed so far: 4.740000 # loops : 50 mean,max change (kT/e) : 2.9327857E-06 4.7969818E-04 energy calculations done at 4.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 14:22:10 4.874u 0.450s 0:26.69 19.9% 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 14:22:12 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: 263 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.737263 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): -25.77600 35.70000 ymin,ymax (A): -19.00900 20.62200 zmin,zma (A): -3.804000 38.55500 x,y,z range (A): 61.47600 39.63100 42.35900 scale (grids/A): 1.737263 object centre (A): 4.962001 0.8065004 17.37550 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 89.92010 90.77242 91.94115 assigned negative charge : -289.0263 centred at (gu) : 89.92514 91.06036 92.39642 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 48491 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17312 grid for indexing accessible points = 1.400000 m= 16187 mr = 33124 m= 1754 mr = 12011 m= 67 mr = 1025 m= 0 mr = 30 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 2158 time to turn everything in is 0.2600000 number of dielectric boundary points 20309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 13764 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) : 0.5790878 object centre at (A) : 4.962001 0.8065004 17.37550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5601400E-03 -2.8374135E-02 midg,1,midg; midg,igrid,midg -1.0727320E-02 -2.1170888E-02 1,midg,midg; igrid,midg,midg -2.6543045E-02 -3.2129668E-02 gauss-seidel spectral radius is 0.9982831 estimated iterations to convergence 192 setup time was (sec) 0.5900000 now iterating at: 14:22:14 rms-change max change #iterations 3.018035 172.5242 at 10iterations 1.281976 52.14370 at 20iterations 0.5506042 23.26483 at 30iterations 0.2351322 9.831039 at 40iterations 0.1001149 4.401066 at 50iterations 4.2663883E-02 1.940683 at 60iterations 1.8207937E-02 0.7456055 at 70iterations 7.7614840E-03 0.3615417 at 80iterations 3.3091286E-03 0.1182046 at 90iterations 1.4178014E-03 5.8788300E-02 at 100iterations 6.0326949E-04 2.3906708E-02 at 110iterations 2.5847607E-04 1.0090709E-02 at 120iterations finished qdiffx linear iterations at : 14:22:24 total time elapsed so far: 11.21000 # loops : 120 mean,max change (kT/e) : 2.5847607E-04 1.0090709E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.34000 DelPhi exited at 14:22:36 11.342u 0.355s 0:24.18 48.3% 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 Wed Dec 21 2011 at 14:22:37 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: 263 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.605895 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): -25.77600 35.70000 ymin,ymax (A): -19.00900 20.62200 zmin,zma (A): -3.804000 38.55500 x,y,z range (A): 61.47600 39.63100 42.35900 scale (grids/A): 2.605895 object centre (A): 4.962001 0.8065004 17.37550 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 89.88015 91.15872 92.91177 assigned negative charge : -289.0263 centred at (gu) : 89.88780 91.59068 93.59468 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 112146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17312 grid for indexing accessible points = 1.400000 m= 54947 mr = 80148 m= 17311 mr = 45235 m= 2958 mr = 14027 m= 264 mr = 2144 m= 15 mr = 183 m= 0 mr = 7 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 7706 time to turn everything in is 0.6000000 number of dielectric boundary points 45897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14107 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) : 1.737263 object centre at (A) : 4.962001 0.8065004 17.37550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0388243E-02 -0.3398895 midg,1,midg; midg,igrid,midg -0.1230707 -0.2539656 1,midg,midg; igrid,midg,midg -0.3337968 -0.3952957 gauss-seidel spectral radius is 0.9991384 estimated iterations to convergence 269 setup time was (sec) 0.9100000 now iterating at: 14:22:39 rms-change max change #iterations 7.356257 288.3759 at 10iterations 4.078755 124.5447 at 20iterations 2.244028 50.63699 at 30iterations 1.232294 28.87847 at 40iterations 0.6768602 16.11475 at 50iterations 0.3716086 8.868317 at 60iterations 0.2038867 4.595488 at 70iterations 0.1117363 2.774895 at 80iterations 6.1245762E-02 1.348248 at 90iterations 3.3475757E-02 0.8393192 at 100iterations 1.8335417E-02 0.4075356 at 110iterations 1.0057854E-02 0.2294407 at 120iterations 5.5204537E-03 0.1176834 at 130iterations 3.0199122E-03 7.0819259E-02 at 140iterations 1.6580073E-03 3.8164377E-02 at 150iterations 9.0722134E-04 2.1099329E-02 at 160iterations 4.9730402E-04 1.1802673E-02 at 170iterations 2.7234165E-04 6.8540573E-03 at 180iterations finished qdiffx linear iterations at : 14:22:55 total time elapsed so far: 16.97000 # loops : 180 mean,max change (kT/e) : 2.7234165E-04 6.8540573E-03 energy calculations done at 16.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.10000 DelPhi exited at 14:23:03 17.098u 0.348s 0:25.56 68.1% 0+0k 0+0io 0pf+0w