On 2/04/2012 10:19 AM, Acoot Brett wrote:
Dear All, I just run a pdb2gmx of a protein, the error message is " Fatal error: Atom CG is used in an interaction of type atom in the topology database, but an atom of that name was not found in residue number 5." According to the sugestion I have tried to find the reason in " http://www.gromacs.org/Documentation/Errors"; But in that part of Document no this error was explained. I am looking forward to getting an explaination from you.
Like it says, look at residue 5 in your .gro and .rtp input files. They need to match well enough.
Mark
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