Sat Oct 8 11:36:26 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 Sat Oct 8 2011 at 11:36:26 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3371 !!! WARNING: HIR 11 has a net charge of 0.5140 !!! WARNING: HIR 13 has a net charge of 0.5140 !!! WARNING: HIR 210 has a net charge of 0.5140 !!! WARNING: HIR 234 has a net charge of 0.5140 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: 0.5849395 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): -29.34300 31.51800 ymin,ymax (A): -25.88800 24.17900 zmin,zma (A): -24.94100 29.53700 x,y,z range (A): 60.86100 50.06700 54.47800 scale (grids/A): 0.5849395 object centre (A): 1.087500 -0.8544998 2.297999 number of atom coordinates read : 3371 total number of charged atoms : 3244 net assigned charge : -3.443992 assigned positive charge : 523.1070 centred at (gu) : 90.03759 90.40531 90.50985 assigned negative charge : -526.5526 centred at (gu) : 90.06093 90.38416 90.42559 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7349 nv = 96 ne = 84 npr = 70108 no. pairs analyzed = 70108 no. exposed pairs = 3744 no. arc points = 25853 no. surface atoms = 1269 nbur = 2102 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 = 1.456000 m= 314 mr = 4326 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.3400000 number of dielectric boundary points 3314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2538 ## 290 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1266449E-09 1.8697526E-09 midg,1,midg; midg,igrid,midg -1.4214642E-09 -2.8304059E-10 1,midg,midg; igrid,midg,midg -1.9335565E-10 -1.6414722E-09 gauss-seidel spectral radius is 0.9849312 estimated iterations to convergence 67 setup time was (sec) 0.5500000 now iterating at: 11:36:27 rms-change max change #iterations 0.1149377 18.99409 at 10iterations 9.1682337E-03 1.296600 at 20iterations 7.5516588E-04 0.1023846 at 30iterations 6.1075123E-05 8.6669922E-03 at 40iterations 5.0881799E-06 6.6757202E-04 at 50iterations finished qdiffx linear iterations at : 11:36:29 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 5.0881799E-06 6.6757202E-04 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.140000 DelPhi exited at 11:36:30 3.144u 0.134s 0:03.73 87.6% 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 Sat Oct 8 2011 at 11:36:30 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3371 !!! WARNING: HIR 11 has a net charge of 0.5140 !!! WARNING: HIR 13 has a net charge of 0.5140 !!! WARNING: HIR 210 has a net charge of 0.5140 !!! WARNING: HIR 234 has a net charge of 0.5140 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: 1.754818 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): -29.34300 31.51800 ymin,ymax (A): -25.88800 24.17900 zmin,zma (A): -24.94100 29.53700 x,y,z range (A): 60.86100 50.06700 54.47800 scale (grids/A): 1.754818 object centre (A): 1.087500 -0.8544998 2.297999 number of atom coordinates read : 3371 total number of charged atoms : 3244 net assigned charge : -3.443992 assigned positive charge : 523.1070 centred at (gu) : 90.11143 91.21490 91.52875 assigned negative charge : -526.5526 centred at (gu) : 90.18226 91.15204 91.27624 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25853 grid for indexing accessible points = 1.400000 m= 26877 mr = 59151 m= 3315 mr = 20228 m= 109 mr = 1981 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 3732 time to turn everything in is 0.5400000 number of dielectric boundary points 30704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 25214 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) : 0.5849395 object centre at (A) : 1.087500 -0.8544998 2.297999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0712479E-03 9.8142680E-03 midg,1,midg; midg,igrid,midg -1.8164586E-02 -9.9516604E-03 1,midg,midg; igrid,midg,midg 8.9393888E-04 -3.0644022E-02 gauss-seidel spectral radius is 0.9984600 estimated iterations to convergence 202 setup time was (sec) 0.8000000 now iterating at: 11:36:31 rms-change max change #iterations 4.270700 206.7136 at 10iterations 1.911730 62.72271 at 20iterations 0.8542092 28.05426 at 30iterations 0.3828955 12.49468 at 40iterations 0.1712455 5.482613 at 50iterations 7.6675296E-02 2.477964 at 60iterations 3.4243312E-02 1.087248 at 70iterations 1.5399450E-02 0.4796581 at 80iterations 6.8787755E-03 0.2048645 at 90iterations 3.0992171E-03 9.6141815E-02 at 100iterations 1.3767697E-03 4.1359901E-02 at 110iterations 6.1980210E-04 1.9019127E-02 at 120iterations finished qdiffx linear iterations at : 11:36:37 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 6.1980210E-04 1.9019127E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 11:36:37 6.958u 0.163s 0:07.47 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 Sat Oct 8 2011 at 11:36:37 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3371 !!! WARNING: HIR 11 has a net charge of 0.5140 !!! WARNING: HIR 13 has a net charge of 0.5140 !!! WARNING: HIR 210 has a net charge of 0.5140 !!! WARNING: HIR 234 has a net charge of 0.5140 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: 2.632227 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): -29.34300 31.51800 ymin,ymax (A): -25.88800 24.17900 zmin,zma (A): -24.94100 29.53700 x,y,z range (A): 60.86100 50.06700 54.47800 scale (grids/A): 2.632227 object centre (A): 1.087500 -0.8544998 2.297999 number of atom coordinates read : 3371 total number of charged atoms : 3244 net assigned charge : -3.443992 assigned positive charge : 523.1070 centred at (gu) : 90.16715 91.82194 92.29310 assigned negative charge : -526.5526 centred at (gu) : 90.27325 91.72794 91.91422 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 190449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25853 grid for indexing accessible points = 1.400000 m= 92116 mr = 144130 m= 28635 mr = 76325 m= 5689 mr = 23185 m= 620 mr = 4243 m= 21 mr = 394 m= 0 mr = 4 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 12369 time to turn everything in is 1.330000 number of dielectric boundary points 69249 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 25945 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) : 1.754818 object centre at (A) : 1.087500 -0.8544998 2.297999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7441621E-02 0.1076815 midg,1,midg; midg,igrid,midg -0.3483275 -0.1827675 1,midg,midg; igrid,midg,midg -9.5774420E-02 -0.4611399 gauss-seidel spectral radius is 0.9992154 estimated iterations to convergence 282 setup time was (sec) 1.620000 now iterating at: 11:36:39 rms-change max change #iterations 10.29827 302.1914 at 10iterations 5.888624 108.6940 at 20iterations 3.360291 68.05830 at 30iterations 1.908594 37.47314 at 40iterations 1.084950 19.90951 at 50iterations 0.6146103 11.32605 at 60iterations 0.3482583 6.653677 at 70iterations 0.1970353 3.452000 at 80iterations 0.1116120 2.017085 at 90iterations 6.3058674E-02 1.078850 at 100iterations 3.5707895E-02 0.6407051 at 110iterations 2.0188754E-02 0.3739042 at 120iterations 1.1418489E-02 0.1954880 at 130iterations 6.4554801E-03 0.1153603 at 140iterations 3.6459803E-03 6.6612244E-02 at 150iterations 2.0612380E-03 3.5306931E-02 at 160iterations 1.1658439E-03 2.0101547E-02 at 170iterations 6.5806898E-04 1.0819435E-02 at 180iterations finished qdiffx linear iterations at : 11:36:49 total time elapsed so far: 11.34000 # loops : 180 mean,max change (kT/e) : 6.5806898E-04 1.0819435E-02 energy calculations done at 11.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.52000 DelPhi exited at 11:36:49 11.522u 0.143s 0:11.99 97.2% 0+0k 0+0io 0pf+0w