I am getting this error "The residues in the chain mg301--gdp302 do not have a consistent type. the first residue has type 'ion', while residue gdp 302 is of type 'other. either there is a mistake in your chain, or it includes nonstandard residue names that have not yet been added to the residue types.dat file in the Gromacs library directory. if there are other molecules such as ligands, they should not have the same chain id as the adjacent protein chain since it's a separate molecule." I have attached the protein file if anyone can help me with this problem.
I would suggest you use CHARMM-GUI to generate topology files to initiate the Gromacs simulation.
Find the link here.
https://www.charmm-gui.org/?doc=input/pdbreader
Put the Mg ion and the GDP in separate chains, GROMACS doesn't like mixed types in the same chain, ... I think.
Kalindu S. Fernando are you suggesting I generate a topology for GDP residue separately?
I assume you haven't made the topology and parameter files for the small molecule, gdp in your case. There is a tutorial for this:
https://www.mdtutorials.com/gmx/complex/index.html
The error occurs due to inconsistent residue types. To fix it:
all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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