Oh good, one problem less! Pavel On 10/29/15 03:55, Smith Liu wrote:

Dear All,

I have it solved. The initial PDB was transformed from a VMD fdvd file. Its Ile contained a CD atom. Once changing CD to CD1, the error message disappears.

Smith

At 2015-10-29 15:24:12, "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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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 This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email. On 1 Nov 2015, at 4:31 am, Pavel Afonine mailto:[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 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]