[gmx-users] How to add calcium ions at desired position?

[Yang Ye]

step 4) shall be add water, minimize energy.
step 5) it's a bad idea to couple ion alone, see wiki pls.
step 6,7) you shall at least have two stages, em, eq before production md.

On 11/19/2007 5:23 AM, Peggy Yao wrote:
> Hi all,
>
> I would like to simulate a protein with calcium ions at the calcium
> binding sties. I cannot use genion to add calcium ions because genion
> put the ions randomly. Is there any conventional way to do this?
>
> The only way I could think of is the following:
>
> 1. Add the calcium ions in the protein PDB input file as HETATM with
> residue name CA2+.
>
> 2. pdb2gmx -f protein_ca.pdb -p protein_ca.top -o protein_ca.gro
>
> 3. In protein_ca.top, the last portions is
> ; Compound    #mols
> Protein_A            1
> Protein_B            1
> Change the last line (Protien_B ...) to: CA2+      2
>
> 4. Minimize energy, and add water.
>
> 5. In md.mdp, set:
> tc-grps = protein sol CA2+
> tau_t = 0.1 0.1 0.1
> ref_t = 300 300 300
>
> 6. grompp -f md.mdp -c protein_ca_water.gro -p protein_ca.top -o md.tpr
>
> 7. mdrun -s md.tpr -o protein.trr -x protein.xtc -c protein.gro
>
> However, after several MD steps, I got the following fatal error:
>
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: nsgrid.c, line: 220
>
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
>
> -------------------------------------------------------
>
> Why it is so? How should I do it? I am a new user of Gromacs, and I've
> been struggling on this issue for an entire day already. I will
> appreciate it very much if someone could help me. Thanks a lot!
>
> Peggy
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