Quoting Peggy Yao <[EMAIL PROTECTED]>: > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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