In GROMACS when I give a PDB file its showing the error that HE1 atom not found in topology. How can I rectify it?

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Danish Jasnaik

HI,

http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database

Hope this helps.

Regards

Aditya Kumar Sarkar

Hi,

Is it possible to identify for which residue GROMACS is showing this error?

Alternatively, if the presence of hydrogen is not very crucial (if there is no pH issue) you can remove this from your input PDB file because in anyway GROMACS will rebuild it.

Hope this help

Aditya