[gmx-users] Method insert ion

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 2 13:03:18 CET 2011



Saeid Akbarshahi wrote:
> If I do not use for insert ions into the water from genion and Ions 
> put in the file pdb whether Gromacs no problem with it ?
> 

genion is not required.  If you provide reasonable ion positions in the system, 
there is no problem.

-Justin

> Whether the behavior of ions such as ions that enter via genion ?
> 
> 4.pdb :
> 
> ATOM      1  CL   CL   145      23.580  24.000  -0.020  1.00  0.00       
>      
> ATOM      2  CL   CL   343      10.530  15.620  16.980  1.00  0.00       
>      
> ATOM      3  CL   CL   344      16.530   6.620  25.980  1.00  0.00       
>      
> ATOM      4  CL   CL   345      16.530  20.620  35.980  1.00  0.00       
>      
> ATOM      5  CL   CL   346      22.530  10.620  13.980  1.00  0.00       
>      
> ATOM      6  CL   CL   347      22.530  20.620  28.980  1.00  0.00       
>      
> ATOM      7  CL   CL   348      20.530   8.020   9.980  1.00  0.00       
>      
> ATOM      8  Na   Na   349      20.530  30.620  31.980  1.00  0.00       
>      
> ATOM      9  Na   Na   350      20.530   4.620  29.980  1.00  0.00       
>      
> ATOM     10  Na   Na   351      15.530  40.620   7.980  1.00  0.00       
>      
> ATOM     11  Na   Na   352      15.530  10.620  19.980  1.00  0.00       
>      
> ATOM     12  Na   Na   353      30.530  16.620  24.980  1.00  0.00       
>      
> ATOM     13  Na   Na   354      40.530  15.620  19.980  1.00  0.00       
>      
> ATOM     14  Na   Na   355      10.530  22.620  34.980  1.00  0.00 
> 
> topol.top  :
> 
> ;
> ; File 'topol.top' was generated
> ; By user: onbekend (0)
> ; On host: onbekend
> ; At date: Wed Nov  2 10:28:56 2011
> ;
> ; This is a standalone topology file
> ;
> ; It was generated using program:
> ; pdb2gmx - VERSION 4.5.5
> ;
> ; Command line was:
> ; pdb2gmx -f 4.pdb -posrefc 0 
> ;
> ; Force field was read from the standard Gromacs share directory.
> ;
> 
> ; Include forcefield parameters
> #include "gromos53a6.ff/forcefield.itp"
> 
> [ moleculetype ]
> ; Name            nrexcl
> Ion                 1
> 
> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass 
>  typeB    chargeB      massB
> ; residue 145 CL  rtp CL   q -1.0
>      1        CL-    145     CL     CL      1         -1     35.453   ; 
> qtot -1
> ; residue 343 CL  rtp CL   q -1.0
>      2        CL-    343     CL     CL      2         -1     35.453   ; 
> qtot -2
> ; residue 344 CL  rtp CL   q -1.0
>      3        CL-    344     CL     CL      3         -1     35.453   ; 
> qtot -3
> ; residue 345 CL  rtp CL   q -1.0
>      4        CL-    345     CL     CL      4         -1     35.453   ; 
> qtot -4
> ; residue 346 CL  rtp CL   q -1.0
>      5        CL-    346     CL     CL      5         -1     35.453   ; 
> qtot -5
> ; residue 347 CL  rtp CL   q -1.0
>      6        CL-    347     CL     CL      6         -1     35.453   ; 
> qtot -6
> ; residue 348 CL  rtp CL   q -1.0
>      7        CL-    348     CL     CL      7         -1     35.453   ; 
> qtot -7
> ; residue 349 Na  rtp NA   q +1.0
>      8        NA+    349     Na     Na      8          1    22.9898   ; 
> qtot -6
> ; residue 350 Na  rtp NA   q +1.0
>      9        NA+    350     Na     Na      9          1    22.9898   ; 
> qtot -5
> ; residue 351 Na  rtp NA   q +1.0
>     10        NA+    351     Na     Na     10          1    22.9898   ; 
> qtot -4
> ; residue 352 Na  rtp NA   q +1.0
>     11        NA+    352     Na     Na     11          1    22.9898   ; 
> qtot -3
> ; residue 353 Na  rtp NA   q +1.0
>     12        NA+    353     Na     Na     12          1    22.9898   ; 
> qtot -2
> ; residue 354 Na  rtp NA   q +1.0
>     13        NA+    354     Na     Na     13          1    22.9898   ; 
> qtot -1
> ; residue 355 Na  rtp NA   q +1.0
>     14        NA+    355     Na     Na     14          1    22.9898   ; 
> qtot 0
> 
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> ; Include water topology
> #include "gromos53a6.ff/spce.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
> 
> ; Include topology for ions
> #include "gromos53a6.ff/ions.itp"
> 
> [ system ]
> ; Name
> Protein in water
> 
> [ molecules ]
> ; Compound        #mols
> Ion                 1
> 
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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