[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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