ram bio wrote:
Dear Gromacs users,
I have a modelled protein whose net charge is +12.69, and I would like
to ionize the protein to make it neutral using genion command, but in
genion command we can add a specific number of postive or negative
charged ions which for my case would not completely neutralize the
system and i learnt from Justin tutorial that we can even neutralize it
using -conc and -neutral options in conjugation. As I am running a
membrane-protein simulation, I would like to know the command which I am
using is correct or not.
genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA+
-nname CL- -nn 12 -neutral
If my command is wrong Please suggest the right one as In future i have
to conjugate SOL and CL- ions to create a special index file.
If your protein has a net charge of +12.69, it is probably wrong. Does anything
in real life have such a net fractional charge?
Go back and evaluate what you have done. Are there missing atoms? Wrong
parameters? The genion command you want to use is fine, but is not suitable for
your system in its current state.
-Justin
Thanks
Ram
------------------------------------------------------------------------
_______________________________________________
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/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/mailing_lists/users.php
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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/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/mailing_lists/users.php
