I want to study the structure changes of proteins in presence and absence of calcium ion. The calcium concentration would be 400mM and the phenomenon of interest is sec. structure changes, local conformations. The protein in about 300 aa and I am thinking of doing 25ns simulation. I wanted to know how to add the calcium ions to simulation. Can anyone guide me on this topic? Or suggest a protocol in doing so? I am using the following paper as my protocol for simulation. I just want to know how to add calcium ions to simulation.
Hello.
You can follow this workflow:
A) Solvate the protein with:
genbox -cp input.gro -cs solvent.gro -p topol.top -o water.gro
B) Introduce an adequate number of ions:
1. grompp -f param.mdp -c water.gro -p topol.top -o ions.tpr
(you can use minimization mdp)
2. genion -s ions.tpr -o ions.gro -p topol.top -pname CA -nn 'number of ions'
You can calculate the number of ions to insert when you know the number of water molecules in your water box.
Best regards.
The simplest method is to replace an appropriate number of water molecules with calcium.
You can use PACKMOL to create a simulation box with the desired concentration of Ca, water and your protein. Check the manual, is pretty easy. VMD has also the possibility of building electrolite solutions, but I have never use it.
Hello.
You can follow this workflow:
A) Solvate the protein with:
genbox -cp input.gro -cs solvent.gro -p topol.top -o water.gro
B) Introduce an adequate number of ions:
1. grompp -f param.mdp -c water.gro -p topol.top -o ions.tpr
(you can use minimization mdp)
2. genion -s ions.tpr -o ions.gro -p topol.top -pname CA -nn 'number of ions'
You can calculate the number of ions to insert when you know the number of water molecules in your water box.
Best regards.
Hello.
Theoretically yes, once you have the H2O2 parameterization it should be straight forward. However, you must find parameterization for H2O2 in PRODRG or in ATB. I've checked and ATB has parameters for it. Check http://compbio.biosci.uq.edu.au/atb/download.py?molid=1969#files
Best regards,
Ricardo Ferreira
regarding the fact that we usually simulate neutral systme , do you mean that we can add for example 3
zinc ions and 3 cl ions ,
or in case where the total cahrge of a protein is -2 , we can add 20 zinc and 18 cl ions, to studty the effect of zinc? or we can simply add extar zinc and the total charge of system is now 18 !
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