[gmx-users] Metal interactions with proteins

Justin Lemkul jalemkul at vt.edu
Thu Nov 16 21:12:50 CET 2017

On 11/16/17 1:53 PM, RAHUL SURESH wrote:
> Dear Justin
> Why is there no aminoacids.rtp file in charmm36ff?

Because the way the CHARMM topology and parameter files are constructed 
makes it nearly impossible to actually write out only certain types of 
molecules, we lumped (almost) everything into one file called 
"merged.rtp." The only exception is the nucleic acid files, which are 
separate (again, by necessity due to how CHARMM works).

> As mentioned before I have added the metal ion parameters in nonbonded.itp,
> ions.ipt and atomtypes.itp. While performing simulation using the command *"gmx
> pdb2gmx -f cu.pdb -o cu.gro -p cu.top" *I receive the following error
> "Residue 'Cu' not found in residue topology database"
> There describe a note* "*
> *Warning: Starting residue Cu43 in chain not identified as Protein/RNA/DNA.
> Problem with chain definition, or missing terminal residues. This chain
> does not appear to contain a recognized chain molecule. If this is
> incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8
> lines of specbond.dat converted successfully".*
> How do i debug this?

It appears pdb2gmx is interpreting your Cu ion as part of the same chain 
as a protein. Separate it using TER or a different chain identifier so 
that pdb2gmx doesn't try to make it some kind of terminus.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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