[gmx-users] Regarding Residue in chain has different type (Other) from starting residue

[Justin Lemkul]

On 10/15/17 2:42 AM, Dilip H N wrote:
> Hello,
> I have a simulations system and by gmx pdb2gmx i am generating the
> topology, but i am getting the warnings as:-
> Identified residue GLY1 as a starting terminus.
> Warning: Residue TMAO12 in chain has different type (Other) from starting
> residue GLY1 (Protein).
> Warning: Residue TMAO13 in chain has different type (Other) from starting
> residue GLY1 (Protein).
> Warning: Residue TMAO14 in chain has different type (Other) from starting
> residue GLY1 (Protein).
> Warning: Residue TMAO15 in chain has different type (Other) from starting
> residue GLY1 (Protein).
> Warning: Residue TMAO16 in chain has different type (Other) from starting
> residue GLY1 (Protein).
> More than 5 unidentified residues at end of chain - disabling further
> warnings.
> Identified residue GLY1 as a ending terminus....
> 
> Topology is generated, but why am i getting this..?? all the parameters for
> tmao, glycine molecules are already prescribed in the .rtp, .atp
> files etc., in forcefield...
> 
> Any suggestions are appreciated...
> 
> 

It means pdb2gmx is interpreting your input as being a single chain and it's 
finding dissimilar residue types (something that's protein and other things that 
are not). There probably isn't any functional consequence to this, but pdb2gmx 
warns users about such cases because there are times when this can cause 
problems or unintended outcomes.

-Justin

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

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