[gmx-users] CA ions

[Paul Buscemi]

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 

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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