Hi Zijian,
For the bellymask, would the syntax be ‘:x>:18’ to freeze all residues beyond 18 Å of residue x?
I’m trying to following the syntax for a distance-based selection given here (
https://amberhub.chpc.utah.edu/atom-mask-selection-syntax/), but my question is: Does SANDER know to update the selection at every frame?
Note that whether the atoms are froze (via ibelly) or simply strongly restrained (via ntr option) is irrelevant for me. I just need to prevent the solvent from evaporating in a non-periodic calculation.
Best,
Matthew
> On Dec 29, 2023, at 6:35 AM, Huang ZiJian <Hzj-0820.outlook.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
> Hi,
>
> "ibelly" is what u need.
>
> Regards,
> Zijian
>
> 发件人: Matthew Guberman-Pfeffer via AMBER <amber.ambermd.org>
> 发送时间: 2023年12月29日 16:17
> 收件人: AMBER Mailing List <amber.ambermd.org>
> 主题: [AMBER] Specifying Restraints Question
>
> Dear Amber Community,
>
> How can I specify that all residues beyond some distance from an active site residue should be restrained, while all residues within the distance threshold are free to move?
>
> For example, a studying using AMBER states:
> "During the QM/MM free energy simulations, residues with any atom within an 18 Å radius of a sphere centered at the Y731:OH atom were allowed to move, with the remaining atoms kept fixed.” (J. Am. Chem. Soc. 2021, 143, 16, 6054–6059)
>
> Best,
> Matthew
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <mailto:AMBER.ambermd.org>
> http://lists.ambermd.org/mailman/listinfo/amber <https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=05%7C02%7Cmatthew.guberman-pfeffer%40uconn.edu%7Cd1b2678147e34d39955908dc08624e71%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638394465666413798%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C41000%7C%7C%7C&sdata=CxcquSD%2FuWM8OYzcEoqc7zpFRVPbTaG9MOeLz%2BnPk4M%3D&reserved=0>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Dec 29 2023 - 08:30:02 PST
