Atomtype Q5 not found error -Go model simulation

[Asharuthra]

Hi, Sir/Ma'am,

I am newbie to cg martini simulation. I cant perform the go model simulation for my trans membrane protein (human beta1 adrenergic receptor-7BU6.pdb), after lipid bilayer membrane insertion. I didn't face any error till membrane insertion.

I performed the minimisation after the lipid bilayer insertion with my trans-membrane protein. I am getting "atom type not found error" every-time.

I didn't get any error after the minimisation of go model trans-membrane protein alone, but with lipid bilayer "atom type not found error" occurred. I tried with both martini and martini beta version itp file. nothing worked out.

Can you suggest me idea how to solve this error? I have included my files and command-line for your perusal transmembrane_protein.zip

Thank you in advance for your help. .

[pckroon]

martini_v3.0.b.3.2.itp is missing a bunch of particle definitions when compared to martini_v3.0.0.itp.

But this is the wrong place to ask about this

[Asharuthra]

Hello, Sir.

Thanks for the reply. I got atom type not found error, after I ran with martini3 ( martini_v3.0.0.itp) also.

On Fri, May 24, 2024 at 3:32 AM Peter C Kroon @.***> wrote:

martini_v3.0.b.3.2.itp is missing a bunch of particle definitions when compared to martini_v3.0.0.itp.

But this is the wrong place to ask about this

— Reply to this email directly, view it on GitHub https://github.com/marrink-lab/vermouth-martinize/issues/598#issuecomment-2129201789, or unsubscribe https://github.com/notifications/unsubscribe-auth/AKSQKADCMESYNBWP5HAF6LLZD4JLBAVCNFSM6AAAAABIHGWUZ6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCMRZGIYDCNZYHE . You are receiving this because you authored the thread.Message ID: @.***>

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Best regards,

Rudhra O,

PhD Scholar,

C/o Prof. Sanjeev Kumar Singh,

CADD & Molecular Modeling Lab,

Department of Bioinformatics,

Alagappa University,

Karaikudi - 630004,

Tamil Nadu, India.