Wed Dec 28 11:01:13 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 11:01:14 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 = 1968 !!! 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: 0.6336662 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): -35.09600 10.37300 ymin,ymax (A): 1.525000 41.70100 zmin,zma (A): 8.0999970E-02 56.26200 x,y,z range (A): 45.46900 40.17600 56.18100 scale (grids/A): 0.6336662 object centre (A): -12.36150 21.61300 28.17150 number of atom coordinates read : 1968 total number of charged atoms : 1768 net assigned charge : -21.95202 assigned positive charge : 263.9205 centred at (gu) : 90.27662 89.38603 89.82362 assigned negative charge : -285.8723 centred at (gu) : 90.17748 89.54141 89.82800 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5345 nv = 96 ne = 84 npr = 40613 no. pairs analyzed = 40613 no. exposed pairs = 2404 no. arc points = 16832 no. surface atoms = 821 nbur = 1147 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3047 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1555 ## 127 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7353282E-08 -2.6023216E-08 midg,1,midg; midg,igrid,midg -1.7706078E-08 -3.3460978E-08 1,midg,midg; igrid,midg,midg -3.1998628E-08 -2.0741213E-08 gauss-seidel spectral radius is 0.9870427 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 11:01:15 rms-change max change #iterations 0.1246694 20.34187 at 10iterations 1.1919007E-02 2.281776 at 20iterations 1.1829254E-03 0.2160187 at 30iterations 1.1255972E-04 1.8112183E-02 at 40iterations 1.1056398E-05 1.6288757E-03 at 50iterations finished qdiffx linear iterations at : 11:01:19 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 1.1056398E-05 1.6288757E-03 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 11:01:19 4.752u 0.466s 0:05.72 91.0% 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 Wed Dec 28 2011 at 11:01:19 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 = 1968 !!! 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: 1.900999 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): -35.09600 10.37300 ymin,ymax (A): 1.525000 41.70100 zmin,zma (A): 8.0999970E-02 56.26200 x,y,z range (A): 45.46900 40.17600 56.18100 scale (grids/A): 1.900999 object centre (A): -12.36150 21.61300 28.17150 number of atom coordinates read : 1968 total number of charged atoms : 1768 net assigned charge : -21.95202 assigned positive charge : 263.9205 centred at (gu) : 90.83022 88.15828 89.47113 assigned negative charge : -285.8723 centred at (gu) : 90.53288 88.62431 89.48415 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 57739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 21925 mr = 40258 m= 3631 mr = 16803 m= 202 mr = 2409 m= 2 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 23943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 13915 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) : 0.6336662 object centre at (A) : -12.36150 21.61300 28.17150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.0451843E-02 -6.0566254E-02 midg,1,midg; midg,igrid,midg -2.9741326E-02 -4.1081555E-02 1,midg,midg; igrid,midg,midg -2.7515747E-02 -3.7802801E-02 gauss-seidel spectral radius is 0.9985551 estimated iterations to convergence 209 setup time was (sec) 0.9600000 now iterating at: 11:01:21 rms-change max change #iterations 3.510765 157.4708 at 10iterations 1.606372 59.86147 at 20iterations 0.7390339 29.49271 at 30iterations 0.3387106 13.15970 at 40iterations 0.1553162 6.190098 at 50iterations 7.1121246E-02 2.525084 at 60iterations 3.2686621E-02 1.094188 at 70iterations 1.4849842E-02 0.5751152 at 80iterations 6.8324436E-03 0.2434921 at 90iterations 3.1303531E-03 0.1061172 at 100iterations 1.4381392E-03 5.1309198E-02 at 110iterations 6.5872277E-04 2.2623062E-02 at 120iterations finished qdiffx linear iterations at : 11:01:32 total time elapsed so far: 12.02000 # loops : 120 mean,max change (kT/e) : 6.5872277E-04 2.2623062E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 11:01:32 12.199u 0.460s 0:13.13 96.3% 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 28 2011 at 11:01:32 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 = 1968 !!! 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: 2.851498 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): -35.09600 10.37300 ymin,ymax (A): 1.525000 41.70100 zmin,zma (A): 8.0999970E-02 56.26200 x,y,z range (A): 45.46900 40.17600 56.18100 scale (grids/A): 2.851498 object centre (A): -12.36150 21.61300 28.17150 number of atom coordinates read : 1968 total number of charged atoms : 1768 net assigned charge : -21.95202 assigned positive charge : 263.9205 centred at (gu) : 91.24554 87.23757 89.20669 assigned negative charge : -285.8723 centred at (gu) : 90.79947 87.93658 89.22637 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 133101 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16832 grid for indexing accessible points = 1.400000 m= 70021 mr = 96870 m= 26559 mr = 58582 m= 6540 mr = 21996 m= 896 mr = 5117 m= 39 mr = 613 m= 0 mr = 18 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 53960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 14140 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) : 1.900999 object centre at (A) : -12.36150 21.61300 28.17150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7873591 -0.9088386 midg,1,midg; midg,igrid,midg -0.3225187 -0.4346339 1,midg,midg; igrid,midg,midg -0.2863596 -0.3948721 gauss-seidel spectral radius is 0.9992197 estimated iterations to convergence 283 setup time was (sec) 1.830000 now iterating at: 11:01:35 rms-change max change #iterations 8.168767 356.3984 at 10iterations 4.655180 115.3439 at 20iterations 2.628622 58.14960 at 30iterations 1.492915 28.79730 at 40iterations 0.8399243 16.50987 at 50iterations 0.4767628 10.31359 at 60iterations 0.2686202 6.457037 at 70iterations 0.1520194 3.029850 at 80iterations 8.6011983E-02 1.794003 at 90iterations 4.8692603E-02 0.9850159 at 100iterations 2.7528433E-02 0.5245590 at 110iterations 1.5551489E-02 0.3237381 at 120iterations 8.7774424E-03 0.1702232 at 130iterations 4.9618934E-03 0.1067276 at 140iterations 2.8063306E-03 5.4479599E-02 at 150iterations 1.5871497E-03 3.2030106E-02 at 160iterations 9.0029481E-04 1.8995762E-02 at 170iterations 5.0906313E-04 1.0425568E-02 at 180iterations finished qdiffx linear iterations at : 11:01:53 total time elapsed so far: 20.18000 # loops : 180 mean,max change (kT/e) : 5.0906313E-04 1.0425568E-02 energy calculations done at 20.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.37000 DelPhi exited at 11:01:55 20.371u 0.523s 0:22.15 94.3% 0+0k 0+0io 0pf+0w