Dear Amber Community,
I am currently utilizing AmberTools 22.0, installed via conda, to prepare the .prmtop, .inpcrd, and the corresponding system in PDB format for a GPCR-ligand complex for MD simulation. I have attached the bash script I use for your reference.

The residue numbering for GPCR adheres to the Ballesteros Weinstein numbering system. Therefore, it is crucial for the output system PDB file to maintain this numbering. However, I’ve noticed that after inputting the original protein PDB (where the residue number starts from, for instance, 66) into AmberTools, the residue numbering in the output system PDB file starts from 1. This discrepancy poses a challenge when identifying key interactions with certain reserved GPCR residues during post-MD analysis.
I am seeking advice on whether there is a feature in AmberTools that can preserve the original residue numbering in the output PDB file.
Any insights or guidance on how to address this issue would be greatly appreciated.
Best regards,
Yu Chen
---------------------------------------------------------
Yu Chen (M.Sc., Frau/Ms)
Ph.D Student
Freie Universität Berlin
Department of Biology, Chemisty, and Pharmacy
Institute of Pharmacy
Research Group Prof. Dr. Gerhard Wolber
Königin-Luise-Str. 2+4 , 14195
Room 180, Front Building
Berlin / Germany
yu.chen.fu-berlin.de
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Received on Fri Jan 26 2024 - 14:00:02 PST
