I have a molecule with MG ions in the pdb file. When I am creating topology file using pdb2gmx, it does not recognize the MG ions (with gromos 54a7 ff). So I created pdb with only protein atoms and ran pdb2gmx to get a topology file (protein.itp) and protein.gro file. I used editconf for the only MG ions pdb and created MG.gro. I copied the contents from MG.gro into protein.gro and named it complex.gro . This file I used to solvate and there was no problem, but when i add ions using
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr I get following error
Fatal error:
number of coordinates in coordinate file (solv.gro, 216418)
does not match topology (topol.top, 216496)
Please someone help me to create a topology for my molecule with Mg ions.
Thanking you.
I would like to suggest you to follow:
https://www.researchgate.net/post/How_to_use_gromacs_pdb2gmx_for_ATP_molecule
and https://www.researchgate.net/post/How_can_we_get_separate_topology_for_ATP_and_Mg_in_GROMACS_for_CHARMM_forcefiled
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