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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
