[gmx-users] Adding Na ions to DPPG

Myunggi Yi myunggi at gmail.com
Tue Oct 28 15:09:49 CET 2008

On Mon, Oct 27, 2008 at 10:21 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Peyman Yamin wrote:
>> On Monday 27 October 2008 15:07, Justin A. Lemkul wrote:
>>> Peyman Yamin wrote:
>>>> On Monday 27 October 2008 14:03, Justin A. Lemkul wrote:
>>>> Actually I'm doing a funny mistake telling I should replace an O with an
>>>> Na! (probably because of high adrenaline level in my blood for the
>>>> deadline is near!) I should just put one Na beside the O I have! I
>>>> simply
>>>> have a PO4 where one O has no H and thus is negative. an Na+ should
>>>> accompany this O.
>>> Well that makes more sense.  I'm assuming you have a DPPG bilayer with
>>> solvent? Or are you simulating a single DPPG in vacuo?  If it's a bilayer
>>> in solution, just use genion; you can even specify exactly how many Na+
>>> you
>>> want using -np.
>>> If the topology organization is confusing you, refer to Chapter 5 of the
>>> manual. If you make a .top for DPPG, you can specify:
>>> [ molecules ]
>>> DPPG    x
>>> NA+     1 (or whatever)
>>> after including the appropriate force field call and ions.itp; the
>>> parameters for all atom types are taken from these files.
>> Well this looks great! I simulate one single DPPG in solvent. and you
>> know, this Na+ is not in solvent but a part of DPPG. So you mean I just make
>> a DPPG with an O which has no H so is minus and then use genion to add Na?
>> will it place the Na aroung O hopefully? I think if I put no H arounf O the
>> prodrg will force me to have it! so I should delete it and replace it with
>> Na? or I should never use the word "replace" at all???
> Well, the Na+ may be associated with DPPG electrostatically, but they are
> still distinct chemical entities.  You can have a DPPG that has a net -1
> charge; certainly all chemical species are not net neutral!  Indeed, genion
> will place Na+ in whatever solvent you choose, but may not necessarily be
> bound to DPPG. Some simulation may show the association, however.

Yes, keep the DPPG. The charge distribution around anionic lipid has been

> And no, don't replace any part of your DPPG.  Because then you don't really
> have DPPG any more do you?
> -Justin
>  Thanks again ;)
>> Peyman
>>  -Justin
>>>  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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Best wishes,

Myunggi Yi
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
myunggi at gmail.com
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