[phenixbb] a question on rotamer restraints

[Tristan Croll]

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
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On 1 Nov 2015, at 4:31 am, Pavel Afonine <pafonine at lbl.gov<mailto:pafonine at lbl.gov>> 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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