Tue Oct 11 03:45:48 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 03:45:48 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6050203 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): -12.27000 37.18000 ymin,ymax (A): -27.13700 21.38100 zmin,zma (A): -13.37500 45.46600 x,y,z range (A): 49.45000 48.51800 58.84100 scale (grids/A): 0.6050203 object centre (A): 12.45500 -2.877999 16.04550 number of atom coordinates read : 3159 total number of charged atoms : 2746 net assigned charge : -0.8379825 assigned positive charge : 439.4224 centred at (gu) : 90.28442 90.81650 92.33683 assigned negative charge : -440.2612 centred at (gu) : 90.08937 90.71290 92.19947 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6896 nv = 96 ne = 84 npr = 59539 no. pairs analyzed = 59539 no. exposed pairs = 3480 no. arc points = 24011 no. surface atoms = 1176 nbur = 1983 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3865 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 3349 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2487 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 8699 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3361177E-09 1.0082897E-08 midg,1,midg; midg,igrid,midg -4.7192676E-09 5.1531850E-09 1,midg,midg; igrid,midg,midg -9.5824806E-09 9.0835206E-09 gauss-seidel spectral radius is 0.9858779 estimated iterations to convergence 69 setup time was (sec) 0.8000000 now iterating at: 03:45:49 rms-change max change #iterations 0.1172473 18.50742 at 10iterations 1.0374929E-02 1.744095 at 20iterations 9.4853563E-04 0.1304092 at 30iterations 9.8272954E-05 2.1064758E-02 at 40iterations 1.4614341E-05 2.4223328E-03 at 50iterations finished qdiffx linear iterations at : 03:45:53 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 1.4614341E-05 2.4223328E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 03:45:54 4.561u 0.395s 0:05.67 87.3% 0+0k 0+0io 4pf+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 03:45:55 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.815061 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): -12.27000 37.18000 ymin,ymax (A): -27.13700 21.38100 zmin,zma (A): -13.37500 45.46600 x,y,z range (A): 49.45000 48.51800 58.84100 scale (grids/A): 1.815061 object centre (A): 12.45500 -2.877999 16.04550 number of atom coordinates read : 3159 total number of charged atoms : 2746 net assigned charge : -0.8379825 assigned positive charge : 439.4224 centred at (gu) : 90.85278 92.44856 97.00967 assigned negative charge : -440.2612 centred at (gu) : 90.26781 92.13804 96.59801 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 74882 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24011 grid for indexing accessible points = 1.400000 m= 26701 mr = 52397 m= 3510 mr = 19833 m= 145 mr = 2024 m= 0 mr = 28 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 30956 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 21428 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) : 0.6050203 object centre at (A) : 12.45500 -2.877999 16.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5931050E-02 1.7964541E-03 midg,1,midg; midg,igrid,midg -9.4433250E-03 -1.3792251E-03 1,midg,midg; igrid,midg,midg -5.5181719E-03 3.5492040E-02 gauss-seidel spectral radius is 0.9985249 estimated iterations to convergence 206 setup time was (sec) 1.100000 now iterating at: 03:45:57 rms-change max change #iterations 4.135468 207.0980 at 10iterations 1.874863 66.27859 at 20iterations 0.8536105 28.98344 at 30iterations 0.3889485 14.41096 at 40iterations 0.1767399 5.405735 at 50iterations 8.0669999E-02 2.599941 at 60iterations 3.6792740E-02 1.442717 at 70iterations 1.6741410E-02 0.5224380 at 80iterations 7.6276357E-03 0.2386341 at 90iterations 3.4707154E-03 0.1068420 at 100iterations 1.5885290E-03 4.9712181E-02 at 110iterations 7.2689488E-04 2.1906316E-02 at 120iterations finished qdiffx linear iterations at : 03:46:08 total time elapsed so far: 12.77000 # loops : 120 mean,max change (kT/e) : 7.2689488E-04 2.1906316E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 03:46:09 12.993u 0.457s 0:13.99 96.0% 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 Tue Oct 11 2011 at 03:46:09 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3159 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.722591 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): -12.27000 37.18000 ymin,ymax (A): -27.13700 21.38100 zmin,zma (A): -13.37500 45.46600 x,y,z range (A): 49.45000 48.51800 58.84100 scale (grids/A): 2.722591 object centre (A): 12.45500 -2.877999 16.04550 number of atom coordinates read : 3159 total number of charged atoms : 2746 net assigned charge : -0.8379825 assigned positive charge : 439.4224 centred at (gu) : 91.27883 93.67278 100.5144 assigned negative charge : -440.2612 centred at (gu) : 90.40169 93.20711 99.89703 start vw surface at 0.1700000 fill in re-entrant regions at 3.470000 boundary points on vw surface= 173551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24011 grid for indexing accessible points = 1.400000 m= 88014 mr = 127154 m= 30248 mr = 72637 m= 6125 mr = 24244 m= 649 mr = 4359 m= 23 mr = 324 m= 0 mr = 6 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 4.780000 number of dielectric boundary points 69886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 4.940000 number of grid points assigned charge 21967 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) : 1.815061 object centre at (A) : 12.45500 -2.877999 16.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.023164 0.1486358 midg,1,midg; midg,igrid,midg -0.1272051 -5.4134592E-02 1,midg,midg; igrid,midg,midg -5.3898823E-02 0.3610856 gauss-seidel spectral radius is 0.9992289 estimated iterations to convergence 284 setup time was (sec) 5.140000 now iterating at: 03:46:15 rms-change max change #iterations 9.833581 382.8643 at 10iterations 5.670222 148.0703 at 20iterations 3.247532 75.52478 at 30iterations 1.859287 42.65145 at 40iterations 1.061026 19.73509 at 50iterations 0.6067911 14.30851 at 60iterations 0.3452841 6.314985 at 70iterations 0.1971164 3.802445 at 80iterations 0.1123549 2.161808 at 90iterations 6.3888453E-02 1.325057 at 100iterations 3.6364209E-02 0.6575146 at 110iterations 2.0706108E-02 0.4225044 at 120iterations 1.1792941E-02 0.2260761 at 130iterations 6.7273309E-03 0.1268234 at 140iterations 3.8428416E-03 6.7552567E-02 at 150iterations 2.2002060E-03 4.0679932E-02 at 160iterations 1.2717802E-03 2.4265289E-02 at 170iterations 7.3913223E-04 1.5163422E-02 at 180iterations finished qdiffx linear iterations at : 03:46:30 total time elapsed so far: 20.69000 # loops : 180 mean,max change (kT/e) : 7.3913223E-04 1.5163422E-02 energy calculations done at 20.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.91000 DelPhi exited at 03:46:31 20.915u 0.468s 0:21.78 98.1% 0+0k 0+0io 0pf+0w