Yu,
pdb4amber is part of AmberTools and produces a file (stdout_renum.txt) that
maps original residue numbers to processed ones; how you would apply this
is something I have never done, as I just work with the shifted portions
and go from there with my analysuis. That being said, I'm sure it can be
done.
Also, the bash script you attached didn't make it across intact, if you can
please resend it and/or include it in the body of the email, that would
be helpful.
Cheers,
Todd
On Fri, Jan 26, 2024 at 3:36 PM Yu Chen via AMBER <amber.ambermd.org> wrote:
> 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 - 14:00:03 PST
