Tue Oct 11 01:13:42 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 01:13:42 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: SEP 216 has a net charge of -0.4750 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6316200 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): 13.93800 70.30100 ymin,ymax (A): -10.99300 43.70800 zmin,zma (A): -17.43400 25.18200 x,y,z range (A): 56.36300 54.70100 42.61600 scale (grids/A): 0.6316200 object centre (A): 42.11950 16.35750 3.874000 number of atom coordinates read : 2606 total number of charged atoms : 2458 net assigned charge : 3.931016 assigned positive charge : 389.8579 centred at (gu) : 91.24025 89.51880 90.18484 assigned negative charge : -385.9275 centred at (gu) : 90.93512 89.69896 90.01585 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6945 nv = 96 ne = 84 npr = 53018 no. pairs analyzed = 53018 no. exposed pairs = 3039 no. arc points = 21304 no. surface atoms = 1030 nbur = 1576 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3979 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 153 time to turn everything in is 0.3000000 number of dielectric boundary points 3265 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2142 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1317076E-08 2.0100485E-08 midg,1,midg; midg,igrid,midg 2.2546740E-08 -1.1547419E-08 1,midg,midg; igrid,midg,midg -1.8985460E-08 4.1006814E-08 gauss-seidel spectral radius is 0.9870136 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 01:13:43 rms-change max change #iterations 0.1394195 21.07545 at 10iterations 1.3725547E-02 2.198128 at 20iterations 1.6382358E-03 0.3142891 at 30iterations 3.1853130E-04 6.8941116E-02 at 40iterations 8.2625018E-05 1.9092560E-02 at 50iterations finished qdiffx linear iterations at : 01:13:45 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 8.2625018E-05 1.9092560E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.290000 DelPhi exited at 01:13:46 3.291u 0.175s 0:03.89 88.9% 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 Tue Oct 11 2011 at 01:13:46 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: SEP 216 has a net charge of -0.4750 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.894860 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): 13.93800 70.30100 ymin,ymax (A): -10.99300 43.70800 zmin,zma (A): -17.43400 25.18200 x,y,z range (A): 56.36300 54.70100 42.61600 scale (grids/A): 1.894860 object centre (A): 42.11950 16.35750 3.874000 number of atom coordinates read : 2606 total number of charged atoms : 2458 net assigned charge : 3.931016 assigned positive charge : 389.8579 centred at (gu) : 93.71999 88.55573 90.55415 assigned negative charge : -385.9275 centred at (gu) : 92.80523 89.09673 90.04718 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75999 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21304 grid for indexing accessible points = 1.400000 m= 26940 mr = 54149 m= 4162 mr = 20295 m= 212 mr = 2736 m= 0 mr = 74 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 4443 time to turn everything in is 0.5300000 number of dielectric boundary points 30059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19352 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) : 0.6316200 object centre at (A) : 42.11950 16.35750 3.874000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9971432E-03 3.2966062E-02 midg,1,midg; midg,igrid,midg 4.5969423E-02 -3.1258367E-02 1,midg,midg; igrid,midg,midg -7.4750029E-02 4.5658713E-03 gauss-seidel spectral radius is 0.9986193 estimated iterations to convergence 213 setup time was (sec) 0.8200000 now iterating at: 01:13:47 rms-change max change #iterations 4.204043 197.7332 at 10iterations 1.956129 64.13820 at 20iterations 0.9120263 29.07640 at 30iterations 0.4258600 14.11308 at 40iterations 0.1994027 6.113079 at 50iterations 9.2672020E-02 2.982128 at 60iterations 4.3628979E-02 1.352034 at 70iterations 2.0367935E-02 0.6043291 at 80iterations 9.5702168E-03 0.2932730 at 90iterations 4.5597656E-03 0.1586189 at 100iterations 2.1992412E-03 7.5225830E-02 at 110iterations 1.1057254E-03 4.2520523E-02 at 120iterations finished qdiffx linear iterations at : 01:13:53 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 1.1057254E-03 4.2520523E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 01:13:54 7.354u 0.215s 0:08.05 93.9% 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 Tue Oct 11 2011 at 01:13:54 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: SEP 216 has a net charge of -0.4750 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: ASP 298 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.842290 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): 13.93800 70.30100 ymin,ymax (A): -10.99300 43.70800 zmin,zma (A): -17.43400 25.18200 x,y,z range (A): 56.36300 54.70100 42.61600 scale (grids/A): 2.842290 object centre (A): 42.11950 16.35750 3.874000 number of atom coordinates read : 2606 total number of charged atoms : 2458 net assigned charge : 3.931016 assigned positive charge : 389.8579 centred at (gu) : 95.57987 87.83342 90.83121 assigned negative charge : -385.9275 centred at (gu) : 94.20767 88.64506 90.07076 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 176000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21304 grid for indexing accessible points = 1.400000 m= 88754 mr = 130788 m= 30962 mr = 73803 m= 7400 mr = 25298 m= 976 mr = 5718 m= 36 mr = 675 m= 0 mr = 8 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 14791 time to turn everything in is 1.300000 number of dielectric boundary points 67838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 19664 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) : 1.894860 object centre at (A) : 42.11950 16.35750 3.874000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6689618E-02 0.3297123 midg,1,midg; midg,igrid,midg 0.6158810 -0.7298353 1,midg,midg; igrid,midg,midg -0.8015436 -7.2635852E-02 gauss-seidel spectral radius is 0.9992510 estimated iterations to convergence 288 setup time was (sec) 1.610000 now iterating at: 01:13:56 rms-change max change #iterations 9.809072 427.8033 at 10iterations 5.686094 131.3286 at 20iterations 3.274858 60.98047 at 30iterations 1.888317 35.34565 at 40iterations 1.082413 21.25281 at 50iterations 0.6210812 10.91583 at 60iterations 0.3566844 6.363439 at 70iterations 0.2042221 4.160810 at 80iterations 0.1170486 2.253609 at 90iterations 6.6978276E-02 1.245668 at 100iterations 3.8433097E-02 0.6960297 at 110iterations 2.2014597E-02 0.4454346 at 120iterations 1.2658178E-02 0.2279968 at 130iterations 7.3043238E-03 0.1406746 at 140iterations 4.2441776E-03 8.4403992E-02 at 150iterations 2.4828399E-03 4.7218323E-02 at 160iterations 1.4921238E-03 3.3620834E-02 at 170iterations 9.2885830E-04 2.1026611E-02 at 180iterations finished qdiffx linear iterations at : 01:14:07 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 9.2885830E-04 2.1026611E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 01:14:08 13.129u 0.221s 0:13.70 97.3% 0+0k 0+0io 0pf+0w