Mon Oct 10 14:01:03 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 Mon Oct 10 2011 at 14:01:03 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4597 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5468006 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): 16.76600 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 61.72500 65.10600 61.30700 scale (grids/A): 0.5468006 object centre (A): 47.62850 151.5870 28.79850 number of atom coordinates read : 4597 total number of charged atoms : 4409 net assigned charge : 2.906038 assigned positive charge : 703.5097 centred at (gu) : 91.71566 89.24345 87.28003 assigned negative charge : -700.6071 centred at (gu) : 91.67652 89.15983 87.29420 start vw surface at 0.2100000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8770 nv = 96 ne = 84 npr = 92962 no. pairs analyzed = 92962 no. exposed pairs = 5504 no. arc points = 38416 no. surface atoms = 1855 nbur = 2742 mkacc time = 0.2300000 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 = 1.568000 m= 399 mr = 4749 m= 0 mr = 18 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3960 ## 520 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11738 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4984718E-10 1.7431298E-11 midg,1,midg; midg,igrid,midg -8.7394553E-10 8.7901847E-10 1,midg,midg; igrid,midg,midg -1.5370036E-10 9.1287322E-10 gauss-seidel spectral radius is 0.9828741 estimated iterations to convergence 63 setup time was (sec) 0.7500000 now iterating at: 14:01:04 rms-change max change #iterations 9.4202302E-02 16.54261 at 10iterations 6.6790134E-03 1.024612 at 20iterations 7.3008635E-04 0.1099930 at 30iterations 1.7931285E-04 2.4042130E-02 at 40iterations 5.4563163E-05 7.8773499E-03 at 50iterations finished qdiffx linear iterations at : 14:01:07 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 5.4563163E-05 7.8773499E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 14:01:08 4.291u 0.257s 0:04.95 91.7% 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 Mon Oct 10 2011 at 14:01:08 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4597 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.640402 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): 16.76600 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 61.72500 65.10600 61.30700 scale (grids/A): 1.640402 object centre (A): 47.62850 151.5870 28.79850 number of atom coordinates read : 4597 total number of charged atoms : 4409 net assigned charge : 2.906038 assigned positive charge : 703.5097 centred at (gu) : 95.14538 87.72892 81.83911 assigned negative charge : -700.6071 centred at (gu) : 95.02944 87.47926 81.88231 start vw surface at 0.2300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 98794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30974 mr = 69392 m= 3540 mr = 21542 m= 120 mr = 1940 m= 0 mr = 23 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 523 time to turn everything in is 0.7800000 number of dielectric boundary points 40531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 447 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 33808 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) : 0.5468006 object centre at (A) : 47.62850 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3712307E-03 9.5337164E-03 midg,1,midg; midg,igrid,midg 1.5139503E-02 3.1628571E-02 1,midg,midg; igrid,midg,midg -1.1535557E-02 -1.4640858E-02 gauss-seidel spectral radius is 0.9983535 estimated iterations to convergence 196 setup time was (sec) 1.120000 now iterating at: 14:01:09 rms-change max change #iterations 4.367526 191.7742 at 10iterations 1.892506 70.37451 at 20iterations 0.8208796 29.95871 at 30iterations 0.3570572 11.46321 at 40iterations 0.1559167 4.738043 at 50iterations 6.7763552E-02 2.130642 at 60iterations 2.9627198E-02 0.8475227 at 70iterations 1.2880856E-02 0.3792591 at 80iterations 5.6373328E-03 0.1688042 at 90iterations 2.4777260E-03 7.2971344E-02 at 100iterations 1.1019036E-03 3.1277657E-02 at 110iterations 4.9723533E-04 1.5243530E-02 at 120iterations finished qdiffx linear iterations at : 14:01:18 total time elapsed so far: 9.650000 # loops : 120 mean,max change (kT/e) : 4.9723533E-04 1.5243530E-02 energy calculations done at 9.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 14:01:18 9.817u 0.259s 0:10.39 96.8% 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 Mon Oct 10 2011 at 14:01:18 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: 373 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4597 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 has a net charge of -2.0000 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: 2.460603 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): 16.76600 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 61.72500 65.10600 61.30700 scale (grids/A): 2.460603 object centre (A): 47.62850 151.5870 28.79850 number of atom coordinates read : 4597 total number of charged atoms : 4409 net assigned charge : 2.906038 assigned positive charge : 703.5097 centred at (gu) : 97.71770 86.59321 77.75839 assigned negative charge : -700.6071 centred at (gu) : 97.54412 86.21893 77.82343 start vw surface at 0.2000000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 230065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107150 mr = 169610 m= 31236 mr = 85506 m= 5836 mr = 23708 m= 501 mr = 4145 m= 21 mr = 296 m= 0 mr = 3 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 1656 time to turn everything in is 1.850000 number of dielectric boundary points 91541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 35241 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) : 1.640402 object centre at (A) : 47.62850 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7846125E-03 0.1968287 midg,1,midg; midg,igrid,midg 0.2329179 0.5653272 1,midg,midg; igrid,midg,midg -0.1603488 -0.2686192 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.200000 now iterating at: 14:01:21 rms-change max change #iterations 11.19875 462.8381 at 10iterations 6.472441 168.8245 at 20iterations 3.720350 73.19202 at 30iterations 2.132949 39.92627 at 40iterations 1.218754 22.28199 at 50iterations 0.6961038 12.63041 at 60iterations 0.3957346 6.835234 at 70iterations 0.2246240 3.898552 at 80iterations 0.1276339 2.301221 at 90iterations 7.2469823E-02 1.271114 at 100iterations 4.0965468E-02 0.7540665 at 110iterations 2.3262413E-02 0.4170208 at 120iterations 1.3189387E-02 0.2230568 at 130iterations 7.4732532E-03 0.1226549 at 140iterations 4.2347261E-03 7.0726395E-02 at 150iterations 2.3989321E-03 4.0809631E-02 at 160iterations 1.3581999E-03 2.2323608E-02 at 170iterations 7.7287864E-04 1.4896631E-02 at 180iterations finished qdiffx linear iterations at : 14:01:34 total time elapsed so far: 15.65000 # loops : 180 mean,max change (kT/e) : 7.7287864E-04 1.4896631E-02 energy calculations done at 15.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.83000 DelPhi exited at 14:01:35 15.828u 0.289s 0:16.84 95.6% 0+0k 0+0io 0pf+0w