Tue Oct 11 06:02:02 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+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 Tue Oct 11 2011 at 06:02:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 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: 0.7058030 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): 19.90600 63.99100 ymin,ymax (A): -3.445000 33.46700 zmin,zma (A): 21.58300 72.02200 x,y,z range (A): 44.08500 36.91200 50.43900 scale (grids/A): 0.7058030 object centre (A): 41.94850 15.01100 46.80250 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 6.500009 assigned positive charge : 312.5840 centred at (gu) : 89.73498 89.77174 88.81406 assigned negative charge : -306.0842 centred at (gu) : 89.85873 89.80920 88.75244 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7151 nv = 96 ne = 84 npr = 40815 no. pairs analyzed = 40815 no. exposed pairs = 2467 no. arc points = 17004 no. surface atoms = 844 nbur = 1217 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4214 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1583 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7751 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9466920E-08 6.4984143E-08 midg,1,midg; midg,igrid,midg 7.3479384E-08 3.3908353E-08 1,midg,midg; igrid,midg,midg 1.1582927E-07 -5.1714903E-09 gauss-seidel spectral radius is 0.9895356 estimated iterations to convergence 80 setup time was (sec) 0.6100000 now iterating at: 06:02:03 rms-change max change #iterations 0.1977480 30.43541 at 10iterations 2.4426499E-02 3.053689 at 20iterations 3.1730947E-03 0.4497585 at 30iterations 5.0409639E-04 7.3724747E-02 at 40iterations 1.2066279E-04 1.4570236E-02 at 50iterations finished qdiffx linear iterations at : 06:02:07 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.2066279E-04 1.4570236E-02 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 06:02:08 4.212u 0.259s 0:06.01 74.2% 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 06:02:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 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: 2.117409 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): 19.90600 63.99100 ymin,ymax (A): -3.445000 33.46700 zmin,zma (A): 21.58300 72.02200 x,y,z range (A): 44.08500 36.91200 50.43900 scale (grids/A): 2.117409 object centre (A): 41.94850 15.01100 46.80250 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 6.500009 assigned positive charge : 312.5840 centred at (gu) : 89.20493 89.31513 86.44215 assigned negative charge : -306.0842 centred at (gu) : 89.57636 89.42778 86.25764 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17004 grid for indexing accessible points = 1.400000 m= 31323 mr = 54473 m= 6269 mr = 24096 m= 583 mr = 4263 m= 16 mr = 317 m= 0 mr = 3 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 30635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15338 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) : 0.7058030 object centre at (A) : 41.94850 15.01100 46.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8400788E-02 5.2946173E-02 midg,1,midg; midg,igrid,midg 2.5869256E-02 1.2440487E-02 1,midg,midg; igrid,midg,midg 3.7309349E-02 2.1269070E-02 gauss-seidel spectral radius is 0.9988242 estimated iterations to convergence 231 setup time was (sec) 1.030000 now iterating at: 06:02:10 rms-change max change #iterations 4.531519 169.1802 at 10iterations 2.245093 75.43941 at 20iterations 1.114765 33.95763 at 30iterations 0.5511629 16.78065 at 40iterations 0.2738542 8.147183 at 50iterations 0.1360903 3.905999 at 60iterations 6.7302264E-02 2.185917 at 70iterations 3.3416040E-02 0.9702713 at 80iterations 1.6623208E-02 0.5062952 at 90iterations 8.3481316E-03 0.2467957 at 100iterations 4.1576908E-03 0.1302896 at 110iterations 2.1112266E-03 6.2536240E-02 at 120iterations finished qdiffx linear iterations at : 06:02:18 total time elapsed so far: 9.400000 # loops : 120 mean,max change (kT/e) : 2.1112266E-03 6.2536240E-02 energy calculations done at 9.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 06:02:19 9.592u 0.265s 0:10.35 95.1% 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 06:02:19 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 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: 3.176114 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): 19.90600 63.99100 ymin,ymax (A): -3.445000 33.46700 zmin,zma (A): 21.58300 72.02200 x,y,z range (A): 44.08500 36.91200 50.43900 scale (grids/A): 3.176114 object centre (A): 41.94850 15.01100 46.80250 number of atom coordinates read : 2061 total number of charged atoms : 1933 net assigned charge : 6.500009 assigned positive charge : 312.5840 centred at (gu) : 88.80743 88.97294 84.66325 assigned negative charge : -306.0842 centred at (gu) : 89.36462 89.14175 84.38645 start vw surface at 0.1800000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 174148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17004 grid for indexing accessible points = 1.400000 m= 96978 mr = 130734 m= 40569 mr = 81465 m= 11865 mr = 33721 m= 2384 mr = 9317 m= 283 mr = 1809 m= 17 mr = 190 m= 0 mr = 12 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.980000 number of dielectric boundary points 68996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 15464 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) : 2.117409 object centre at (A) : 41.94850 15.01100 46.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1296833 0.3820038 midg,1,midg; midg,igrid,midg 0.2066487 8.7393090E-02 1,midg,midg; igrid,midg,midg 0.3405641 0.3423115 gauss-seidel spectral radius is 0.9992927 estimated iterations to convergence 297 setup time was (sec) 2.310000 now iterating at: 06:02:21 rms-change max change #iterations 10.17430 335.0336 at 10iterations 6.026621 127.2203 at 20iterations 3.557482 94.84129 at 30iterations 2.101039 41.31847 at 40iterations 1.236534 24.22275 at 50iterations 0.7249845 13.90025 at 60iterations 0.4258186 8.687662 at 70iterations 0.2494545 4.720886 at 80iterations 0.1463556 3.159866 at 90iterations 8.5729577E-02 2.175312 at 100iterations 5.0199836E-02 0.9754486 at 110iterations 2.9414389E-02 0.5057334 at 120iterations 1.7385736E-02 0.2997535 at 130iterations 1.0389453E-02 0.1940594 at 140iterations 6.2921401E-03 0.1115792 at 150iterations 3.9339792E-03 7.6103210E-02 at 160iterations 2.5691960E-03 4.3167114E-02 at 170iterations 1.7871589E-03 2.8697968E-02 at 180iterations finished qdiffx linear iterations at : 06:02:35 total time elapsed so far: 15.56000 # loops : 180 mean,max change (kT/e) : 1.7871589E-03 2.8697968E-02 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 06:02:35 15.740u 0.269s 0:16.33 97.9% 0+0k 0+0io 0pf+0w