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Deprotonated LYR(Retinal+LYS) in CHARMM-GUI
#38237 03/26/21 11:50 AM
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cqcqxq Offline OP
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Here are the .ret and .prm files of the engineered deprotonated LYR(ChR2) which can be recognized by ChARMM-GUI.
And they refer to this file(toppar_all36_prot_retinol.str) and this paper(Zhu S, Brown MF, Feller SE. Retinal conformation governs pKa of protonated Schiff base in rhodopsin activation. J Am Chem Soc. 2013 Jun 26;135(25):9391-8. doi: 10.1021/ja4002986. Epub 2013 Jun 11. PMID: 23701524; PMCID: PMC5176254.).

Hope it will help and use at your own risk !!!
Look forward to your suggestions!
Feel free to ask or contact. Email: 2016212287@stu.cqupt.edu.cn

Attached Files
LYR.zip (2.4 KB, 36 downloads)
SHA1: 354d0fc27c5b16fc6ea3d42fb5ea7508a71bbede
Last edited by cqcqxq; 03/26/21 01:27 PM.
Re: Deprotonated LYR(Retinal+LYS) in CHARMM-GUI
cqcqxq #38239 03/28/21 05:35 PM
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How, and why, does it differ from LYR in toppar_all36_prot_retinol.str ?
How was this developed?
What is a ".ret" file?


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden
Re: Deprotonated LYR(Retinal+LYS) in CHARMM-GUI
lennart #38240 03/29/21 01:39 PM
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I'm so sorry! The ".ret" means ".rtf" file. That was a writing blunder.
Achieve this by above-mentioned references.
It's different from the LYR in toppar_all36_prot_retinol.str which makes every LYR protonated. However, LYR needs to be deprotonated at times.
It's developed by understanding the charmm ff and referring to literature. And it can be used in CHARMM-GUI with engineered residues option(PDB reader or Membrane Builder). You can get a deprotonated LYR when you upload "LYR.zip".


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