[gmx-users] CA ions

[Justin Lemkul]

On 12/7/19 11:41 AM, Paul Buscemi wrote:
> Can you not use pdb2gmx with a pdb of Ca. Then create the itp from the new top. Add that as an include. Need to do the same with Cl for charge neutrality

It's not even necessarily that complicated. All the force fields in 
GROMACS support Ca2+ either in .rtp or ions.itp files.

If there are structured ions (e.g. specifically coordinated to the 
protein), then pdb2gmx will handle that automatically. If ions need to 
be added to the solution, it's as simple as using -pname with -pq 2.

-Justin

> PB
>
>> On Dec 6, 2019, at 7:34 PM, Tasneem Kausar <tasneemkausar12 at gmail.com> wrote:
>>
>> You are going to the right way. There are more options given in gmx genion.
>> Check -pname and -nname. These options will help you to select the name of
>> positive and negative ions.
>>
>>
>>> On Sat, 7 Dec 2019, 5:05 am Iman Katouzian, <imaneternity at gmail.com> wrote:
>>>
>>> Good day,
>>>
>>> I want to simulate my protein in gromacs and in this simulation I need to
>>> add a certain concentration of CA ions to my system. However, I have no
>>> idea about how to do this so first I have to neutralize my system and then
>>> need to add the needed CA ions which act as binding agents* (necessary
>>> factor in experiments) *in my protein. I have heard that with -neutral and
>>> -conc for adding the certain concentration I can do this thing.
>>> I would appreciate it if somebody can help me with this issue.
>>>
>>> Thanks.
>>> --
>>>
>>> *Iman Katouzian*
>>>
>>> *Ph.D.** candidate of Food Process Engineering*
>>>
>>> *Faculty of Food Science and Technology*
>>>
>>> *University of Agricultural Sciences and Natural Resources, Gorgan, Iran*
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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