[gmx-users] Method insert ion
Saeid Akbarshahi
saeidakbarshahi at yahoo.com
Wed Nov 2 12:06:53 CET 2011
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 ?
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
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