[gmx-users] Fix the residues

[liming_52]

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