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

Peggy Yao peggy.yao at gmail.com
Sun Nov 18 22:23:10 CET 2007

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!


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