Anselm,
Thank you for your suggestion to use CYX as the branching point. I have the parameters for the linkers (from antechamber) and tleap is not complaining about the branching. However, it gives an error message when checking the structure:
Error: Could not find angle parameter: S - CT - C
Error: Could not find angle parameter: S - CT - HC
Error: Could not find angle parameter: S - CT - HC
Looks like it's having trouble with the bonds around the sulfur in the CYX residue. I have loaded gaff and gaff2 but it still gives this error. Can you think of a way to get around this?
Thank you!
Sasha
---
Oleksandr “Sasha” Buzko
Computational Biology
ImmunityBio
9922 Jefferson Blvd
Culver City, CA 90230
Mobile: 858-531-0646
-----Original Message-----
From: Dr. Anselm Horn via AMBER <amber.ambermd.org>
Sent: Monday, February 26, 2024 5:53 AM
To: amber.ambermd.org
Subject: Re: [AMBER] Is it possible to model a protein with a linker covalently attached at a cysteine?
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Sasha,
I'd suggest to create actual parameters for modified residues, i.e.
model the two peptides as two chains, and create parameters for the linking moiety: either treat it as modified cysteine residue with branching ability like CYX or, depending on the chemical nature of your linker, reuse the CYX residue and create an additional linking residue.
Of course, you need to generate suitable parameters and atomic charges for your system. But you had a full MM description then and not just an harmonic constraint between two molecules. However, it also depends on your actual research question.
We used a somehow similar approach before (see 10.1021/acs.jmedchem.1c01574; supplement p.22f). If you need more specific support for your system, feel free to contact me off-list.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) Germany
Am 26.02.2024 um 05:27 schrieb Sasha Buzko via AMBER:
> Dear Amber users,
> I'm trying to model a system that consists of a protein, a non-peptide linker covalently bound to a cysteine and a short peptide covalently bound to the other end of the linker.
> Since this system is effectively branched, I'm trying to figure out how to set it up.
>
> I've tried treating the protein and the linked peptide as two separate chains and using restraints on the cysteine and the bonded functional group of the linker to hold them together. For example:
> Restraint group 1 # During the heating phase, restraining all protein
> atoms
> 100.0
> RES 1 29 31 618
> END
> Restraint group 2 # The restrained residues in question have a higher
> value that is used everywhere
> 1000.0
> RES 30 30 619 619
> END
> END
>
> The restrained linker keeps drifting off sooner or later. It may hold in place during most of the equilibration but when it hits production the linked structure floats away eventually. It happens both in explicit (TIP3P, OPC or TIP4PEW) and implicit solvent. I am setting the ntr=1 flag everywhere.
>
> I've also attempted to use the ibelly option but this one is not usable with the GPU implementation and even in many cases on CPU.
>
> Finally, I'm trying to define the entire linked structure as a non-standard amino acid and run it through antechamber. But this is predictably taking forever and is not going to be practical even if it works. Besides, not sure about the accuracy of the charges for amino acids that will come out of it.
>
> Has anyone had to deal with something like this? Am I missing something or is this the limit of the restraint function? Maybe there is a better way to approach this?
>
> Thank you in advance for any suggestions.
>
> Sasha
>
>
>
>
> ---
> Oleksandr "Sasha" Buzko
> Computational Biology
> ImmunityBio
> 9922 Jefferson Blvd
> Culver City, CA 90230
>
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Received on Mon Feb 26 2024 - 10:00:02 PST
