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+
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 wrote:
>
> You are going to the right way. There are more options given in gmx genion.
>
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, wrote:
> Good day,
>
> I want to simulate my protein in gromacs and in
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*
