This is actually a CHARMM thing rather than a VMD thing: in ILE, CD1 becomes CD for whatever reason. There are other naming mismatches - primarily in the hydrogens for protein and nucleic acids, but becoming more numerous as you get further off the beaten track.

Cheers,

Tristan

Tristan Croll

Lecturer

Faculty of Health

School of Biomedical Sciences

Institute of Health and Biomedical Engineering

Queensland University of Technology

60 Musk Ave

Kelvin Grove QLD 4059 Australia

+61 7 3138 6443

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On 1 Nov 2015, at 4:31 am, Pavel Afonine <[email protected]> wrote:

Hi Smith,

can you please send me the PDB file?

Pavel

On 10/29/15 00:24, Smith Lee wrote:
Dear All,

When I run phenix.real_space_refine, in the rotamer restraints step I meet the following error message:

RuntimeError: rotatable bond atoms CG1-CD (as defined by tardy-tree): no match in rotamer-info.tor_ids

Will you please let me know how to overcome this error?

Best regards.

Smith
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