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

[Justin A. Lemkul]

Quoting Peggy Yao <peggy.yao at gmail.com>:

> 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

Never couple solvent and ions separately.  Check out:

http://wiki.gromacs.org/index.php/Thermostats

Try tc-grps = Protein Non-protein

>
> 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.
>
> -------------------------------------------------------

Is this your production step?  Did you minimize after adding the water or run
any equilibration steps?

-Justin

>
> 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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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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