Peyman Yamin wrote:
Dear GMX users,
I want to add sodium ions (Na+) to a phospholipid (DPPG) I have the structure
with the Na replaced with O. I get a .top with this from prodrg and try to
add the Na manually at the right place by removing the corresponding O. I use
GROMOS 96.1 forcefield. GMX version 3.3.1. I have a problem:
Are you trying to replace the O in DPPG with Na+? Or are you simply trying to
add ions to the surrounding solvent (water)? If you just need ions in the
solvent, use genion; you don't have to do it manually.
* In .top file, as far as I can understand, I should just replace OA with NA+
and set the mass and charge.
DPPG has a centre: [ O-P(O)=O ] -
The Na+ should be around this with +1 charge.
should I put charge +1 ?
Again, I'm not clear on what you're trying to accomplish. If you replace one of
these oxygen atoms, you will likely not have an integer charge within the DPPG
molecule itself.
* which parameters should I place in the top as the Na+ is not bonding. I need
LJ and Coulomb params. I have C6 and C12 them from ffG43a1nb.itp. (NA+ OA)
but I'm not sure where should I put it in the top file. What should I insert
manually in top file at all?
Simply #include "ffG43a1.itp" at the top of your .top file; it will include
nonbonded and bonded parameters for all the atoms in the system.
-Justin
Thanks in advance for the time,
I've been away for some time from GMX and might sound
Cheers,
Peyman
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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