Justin A. Lemkul wrote:
errabah fatima ezzahra wrote:
i added the NA using the genion
*
genion -s em.tpr -o waterbox_ions.gro -np 6 , and i added the NA
to the topology file , subtracted the water number by 6. tail
waterbox_ions.gro file have this
3567W W 3789 1.256 3.600 3.784
3568W W 3790 2.491 6.539 2.341
3569W W 3791 2.432 6.349 3.116
3570NA NA 3792 2.677 4.903 3.617
3571NA NA 3793 0.466 3.245 4.787
3572NA NA 3794 6.028 4.147 2.550
3573NA NA 3795 3.201 1.027 5.879
3574NA NA 3796 1.677 1.849 6.641
3575NA NA 3797 5.729 5.645 7.089
and the topology file
#include "martini_v2.1.itp"
#include "1pef.itp"
#include "martini_v2.0_ions.itp"
[ system ]
; Name
PEPTIDE F
[ molecules ]
; Compound #mols
Protein 6
W 3551
NA+6
This looks fine. There are other things I suggested you look at; you
haven't ruled out that something else went wrong along the way or that
your peptide doesn't have the net charge you think it does.
Actually, no it doesn't. You don't have any space between the moleculetype name
("NA+") and the number of molecules. This line isn't being read correctly,
which might be your problem, though I'm shocked that you're not getting some
other error about a missing number of molecules or number of coordinates not
matching the topology.
-Justin
--
========================================
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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