Tue Oct 11 08:19:03 PDT 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 Tue Oct 11 2011 at 08:19:03 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3113 !!! WARNING: GLM 342 has a net charge of -0.0940 !!! WARNING: HIR 384 has a net charge of 0.5140 !!! WARNING: ASN 491 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5771164 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 0.5771164 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3113 total number of charged atoms : 2971 net assigned charge : -6.351975 assigned positive charge : 466.0049 centred at (gu) : 90.99138 89.34142 89.96767 assigned negative charge : -472.3580 centred at (gu) : 90.96353 89.31379 90.01456 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6756 nv = 96 ne = 84 npr = 63955 no. pairs analyzed = 63955 no. exposed pairs = 3962 no. arc points = 27320 no. surface atoms = 1331 nbur = 1782 mkacc time = 0.1500000 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= 316 mr = 3578 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3483 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2853 ## 321 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6767563E-10 -2.2400048E-09 midg,1,midg; midg,igrid,midg -2.1496147E-09 -5.8197330E-10 1,midg,midg; igrid,midg,midg -1.4718570E-09 -8.2790197E-10 gauss-seidel spectral radius is 0.9845143 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 08:19:04 rms-change max change #iterations 0.1022272 15.94046 at 10iterations 7.9812519E-03 1.110394 at 20iterations 9.6941099E-04 0.1480944 at 30iterations 2.6650171E-04 4.0198326E-02 at 40iterations 9.0423535E-05 1.3831139E-02 at 50iterations finished qdiffx linear iterations at : 08:19:07 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 9.0423535E-05 1.3831139E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:19:08 3.391u 0.139s 0:04.06 86.6% 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 Tue Oct 11 2011 at 08:19:08 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3113 !!! WARNING: GLM 342 has a net charge of -0.0940 !!! WARNING: HIR 384 has a net charge of 0.5140 !!! WARNING: ASN 491 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.731349 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 1.731349 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3113 total number of charged atoms : 2971 net assigned charge : -6.351975 assigned positive charge : 466.0049 centred at (gu) : 92.97371 88.02372 89.90216 assigned negative charge : -472.3580 centred at (gu) : 92.89020 87.94109 90.04369 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 74084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27320 grid for indexing accessible points = 1.400000 m= 25082 mr = 50660 m= 3216 mr = 17693 m= 119 mr = 1743 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1323 time to turn everything in is 0.5500000 number of dielectric boundary points 32388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 285 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 23045 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) : 0.5771164 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5727432E-02 -3.3599649E-02 midg,1,midg; midg,igrid,midg -8.3550289E-03 3.2231682E-03 1,midg,midg; igrid,midg,midg -1.1377201E-02 2.6317902E-03 gauss-seidel spectral radius is 0.9984058 estimated iterations to convergence 199 setup time was (sec) 0.8400000 now iterating at: 08:19:09 rms-change max change #iterations 3.915599 179.0441 at 10iterations 1.720964 62.43677 at 20iterations 0.7551723 25.37955 at 30iterations 0.3336743 10.67188 at 40iterations 0.1468176 4.602390 at 50iterations 6.4850755E-02 2.514889 at 60iterations 2.8582079E-02 0.9326916 at 70iterations 1.2660711E-02 0.3940334 at 80iterations 5.6574708E-03 0.1909180 at 90iterations 2.5962831E-03 9.6955776E-02 at 100iterations 1.2486973E-03 5.4372787E-02 at 110iterations 6.3975266E-04 2.2913694E-02 at 120iterations finished qdiffx linear iterations at : 08:19:15 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 6.3975266E-04 2.2913694E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 08:19:16 7.651u 0.172s 0:08.27 94.5% 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 Tue Oct 11 2011 at 08:19:16 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3113 !!! WARNING: GLM 342 has a net charge of -0.0940 !!! WARNING: HIR 384 has a net charge of 0.5140 !!! WARNING: ASN 491 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.597024 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 2.597024 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3113 total number of charged atoms : 2971 net assigned charge : -6.351975 assigned positive charge : 466.0049 centred at (gu) : 94.46030 87.03526 89.85281 assigned negative charge : -472.3580 centred at (gu) : 94.33512 86.91145 90.06530 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 171397 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27320 grid for indexing accessible points = 1.400000 m= 83582 mr = 123310 m= 27247 mr = 66876 m= 5387 mr = 21010 m= 504 mr = 3724 m= 7 mr = 243 m= 0 mr = 2 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 4770 time to turn everything in is 1.420000 number of dielectric boundary points 72959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 23757 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) : 1.731349 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3433943 -0.3848383 midg,1,midg; midg,igrid,midg 5.9054818E-02 2.4715696E-02 1,midg,midg; igrid,midg,midg -0.2174279 0.1125829 gauss-seidel spectral radius is 0.9992083 estimated iterations to convergence 281 setup time was (sec) 1.720000 now iterating at: 08:19:18 rms-change max change #iterations 9.686040 294.1085 at 10iterations 5.624198 151.5210 at 20iterations 3.223617 68.68240 at 30iterations 1.848551 39.00605 at 40iterations 1.050333 20.92644 at 50iterations 0.5972775 12.39474 at 60iterations 0.3393651 6.990540 at 70iterations 0.1923051 4.588337 at 80iterations 0.1086987 2.143187 at 90iterations 6.1599918E-02 1.182693 at 100iterations 3.4930743E-02 0.6518574 at 110iterations 1.9678738E-02 0.4168625 at 120iterations 1.1193858E-02 0.2233522 at 130iterations 6.3680075E-03 0.1245670 at 140iterations 3.6445616E-03 7.4462891E-02 at 150iterations 2.1181577E-03 4.2758942E-02 at 160iterations 1.2614891E-03 2.4061203E-02 at 170iterations 7.8242767E-04 1.6698837E-02 at 180iterations finished qdiffx linear iterations at : 08:19:29 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 7.8242767E-04 1.6698837E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 08:19:30 13.308u 0.194s 0:14.26 94.6% 0+0k 0+0io 0pf+0w