VMD-L Mailing List

From: Stefan Lyne Oliver (sloliver_at_stanford.edu)
Date: Wed Mar 01 2023 - 13:41:26 CST

Dear VMD-L Mailing List,

I've stumbled across an issue with saving coordinates from an MDFF simulation. I'm using MDFF to fit a macromolecular structure (13 subunits; original pdb file - VZV-7bw6-2Penton-Hexons-Triplexes_20230225_01.pdb) into a cryo-EM map (VZV-7bw6-2Penton-Hexons-Triplexes_20230225_01.situs). The NAMD simulation ran to completion and the trajectory files could be visualized in VMD. However, when saving a PDB file of the last frame of the trajectory, any atom numbers beyond 99999 appear to be translated to a hexadecimal format (pdb file - VZV-7bw6-2Penton-Hexons-Triplexes_20230225_01-namd.pdb). This leads to duplicate atom names and causes issues in both Chimera and ChimeraX. The issue appears to come from how Autopsf names atoms beyond 99999; it replaces them with *****. VMD seems to be able to handle this naming convention but this does not translate to the coordinates of the saved pdb file. Is there a workaround for this issue? I didn't see anything on the mailing list but I might have missed it.

I've uploaded all of the files used for the MDFF simulation to my Google Drive account for analysis https://urldefense.com/v3/__https://drive.google.com/drive/folders/1vEz_1wwimhSYeHuSM4Jl0KrsZzMjDFWj?usp=sharing__;!!DZ3fjg!9qj82GmDpqH4D0nEeO4Oc1vLxzldPfenerNEqQ5zPSLBhFBcq2oOv_TwPEpkRoJeGGR60kX1JWYhmpG2BbdN9_4$

Thanks in advance for your help.

Cheers,

Stefan
Stefan Oliver, Ph.D.<https://urldefense.com/v3/__https://profiles.stanford.edu/stefan-oliver__;!!DZ3fjg!9qj82GmDpqH4D0nEeO4Oc1vLxzldPfenerNEqQ5zPSLBhFBcq2oOv_TwPEpkRoJeGGR60kX1JWYhmpG2YlY9K9g$ >
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E-mail: sloliver_at_stanford.edu<mailto:sloliver_at_stanford.edu> Tel: (+1) 650 725 6555
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