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The pdb writer module for OpenMM seems not to write the fourth character for residue names that come in four characters. The input files for my studies are in gromacs file formats. For example for mixed lipids DOPE and DOPG are all read in but are written as the same residue name DOP. Have you noticed this type of error? Any recommendations on howto fix it. Thanks.

Could you post a file that has the problem? I just checked the code for the PDB writer and it looks fine. More likely it has to do with reading your input file.

Peter