Hi Anselm,
This makes a lot sense! Thank you!
Yes, this should be the only place the default generated prmtop record some information related to the chain association.
It is still not possible to know the mapping of chain id if the chain id does not start from A or is not continuous. (say the ligand chain is named X)
I plan to adapt David's idea to use the `add_pdb` application from Amber to add those info in using the same dry PDB as used for tleap.
All the Best,
QZ
________________________________
发件人: Dr. Anselm Horn via AMBER <amber.ambermd.org>
发送时间: 2024年1月24日 10:44
收件人: amber.ambermd.org <amber.ambermd.org>
主题: Re: [AMBER] 回复: [Sender Not Verified] Chain info in .prmtop file
Hi Qianzhen,
maybe the conversion program uses the following entry from the top file:
%FLAG ATOMS_PER_MOLECULE
%FORMAT(10I8)
Using those numbers, one could simply run a counter for each molecule
(=chain).
Just a guess...
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 01/24/2024 05:23 PM, Shao, Qianzhen via AMBER wrote:
> Hi Thomas,
>
> Thanks for sharing!
> Yes, my version of Amber also eraser the chain ids but if I convert the prmtop to a pdb file (say using a made-up inpcrd file with all 0.0) it knows where to add the "TER" mark. I wonder which information in the file lead to that.
>
> All the Best,
> QZ
> ________________________________
> 发件人: Steinbrecher, Thomas <thomas.steinbrecher.roche.com>
> 发送时间: 2024年1月24日 1:23
> 收件人: Shao, Qianzhen <qianzhen.shao.vanderbilt.edu>; AMBER Mailing List <amber.ambermd.org>
> 主题: Re: [Sender Not Verified] [AMBER] Chain info in .prmtop file
>
> 你通常不会收到来自 thomas.steinbrecher.roche.com 的电子邮件。了解这一点为什么很重要<https://aka.ms/LearnAboutSenderIdentification>
> Hi Qianzhen,
>
> time may have proven me wrong here, but in my days of Amber usage long past, this information was not recorded in the prmtop, Amber used to erase chain info and works on a 'list of residues' level only.
>
> Kind Regards,
>
> Thomas
>
>
> On Wed, Jan 24, 2024 at 6:57 AM Shao, Qianzhen via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
> **Warning** The sender address ("Shao, Qianzhen via AMBER" ) can not be verified, sender email address could be spoofed. Please take care to proceed.
> Dear Mailing List,
>
> I'm writing a python parser for .prmtop file right now. I'm having a hard time finding how prmtop record the chain-association for each residue. (i.e.: whether 2 residues are from the same chain)
> I will be grateful if anyone can share some insights.
> Thanks in advance.
>
> All the Best,
> QZ
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Received on Wed Jan 24 2024 - 19:00:02 PST
