[gmx-users] Fix the residues

[Amir Zeb]

Is TYR and SER are N-terminal and C-terminal residues , respectively?
Also, you may compare the corresponding atoms of each residues with same
residues present in your system and does not show the mentioned warning.

All the best

On Fri, Jan 6, 2017 at 10:58 AM, liming_52 <liming_52 at 163.com> wrote:

> Dear Gromacs users,
>
> I am trying to run a md using 4n6p.cif, which was obtained from PDB. I
> converted the file into pdb format using DS4.1, and got the file named
> lactoferrin.pdb. When I directly run
> the command "gmx pdb2gmx -f lactoferrin.pdb -o lactoferrin.gro -water
> spce", the program runs and produces the information as follows:
> ...
> WARNING: WARNING: Residue 1 named TYR of a molecule in the input file was
> mapped
> to an entry in the topology database, but the atom H used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> WARNING: WARNING: Residue 335 named SER of a molecule in the input file
> was mapped
> to an entry in the topology database, but the atom O used in
> an interaction of type angle in that entry is not found in the
> input file. Perhaps your atom and/or residue naming needs to be
> fixed.
>
> ...
> How should I fix the residues? And which tools should I use? Is there any
> examples or tutorials?
>
> If anyone can suggest a solution to this issue, it would be really helpful.
>
>
>
>
>
>
>
> --
>
> With my best wishes,
> Ming Li, PhD
> Chinese Academy of Agricultural Sciences, Beijing, China
> --
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