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.
-Justin
------------------------------------------------------------------------
*De :* Justin A. Lemkul <jalem...@vt.edu>
*À :* Discussion list for GROMACS users <gmx-users@gromacs.org>
*Envoyé le :* Mercredi 13 Juillet 2011 13h05
*Objet :* Re: [gmx-users] Adding Ions
errabah fatima ezzahra wrote:
>
> Hi All,
>
>
> I have a peptide that has three positive charged amino acids (LYS)
and four negative charged amino acids (GLU) consequently it is a
negative peptide. is that right
Assuming typical protonation states, and further assuming that there are
no other unbalanced charges in the peptides, yes.
> when i run gromacs simualtion grompp DOES NOT gave a warning: System
has non-zero total charge: -6 ( i have six peptides)
>
Then you do not have what you think you do. Look at the topology to see
what the net charge on each peptide is and determine whether or not this
is what you want.
> i tried neutralising the system, since that the peptides have an
extra -1 charge per peptide.
>
> however when i did add 6 NA to the system , after running the enrgy
minimization there was an error that System has non-zero total charge:
-6.000000e+00
>
> so i dont understand how by adding 6 positive ions that cause the
negative charge??
>
It can't. You've probably confused which files you're using or are
misreading some output somewhere along the way. Adding six positives
cannot give six negatives.
-Justin
> thank you so much for your help
>
> FZ
>
>
-- ========================================
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
========================================
-- gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists