I tried it and can confirm that leap does not add cmaps to the terminal
ALA for this cyclized system. This seems to be an issue in leap when the
system is built, and should be fixable, we just need to teach leap about
looking for circular systems.I don't know any reason that would prevent it
from working in simulations if the prmtop includes the correct information.
I'll have to look into this more and get back to you.
carlos
On Fri, Feb 17, 2023 at 7:53 PM Ho, Minh <Minh.Ho.tufts.edu> wrote:
> Hi Carlos,
>
> The cyclic peptide is backbone cyclized, meaning the N-terminal of ALA1 is
> covalently linked to the C-terminal of ALA6. The terminal residues are just
> regular L-Ala. Thank you very much for your help.
>
> Best,
> Minh
>
>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Friday, February 17, 2023 7:30 PM
> *To:* Ho, Minh <Minh.Ho.tufts.edu>; AMBER Mailing List <amber.ambermd.org>
> *Subject:* [External] Re: [AMBER] Using amber19sb forcefield to simulate
> cyclic peptide
>
> When you say it is cyclic, how is the connection made? Is the backbone
> circular, or a crosslink with disulfide or similar? What are the details of
> the terminal residues?
> Let me know and we can help you get this working. Should be
> straightforward.
>
> On Fri, Feb 17, 2023, 5:56 PM Ho, Minh via AMBER <amber.ambermd.org>
> wrote:
>
> Hello,
>
> I want to simulate a cyclic peptide with sequence (ALA-ALA-ALA-ALA-ALA)
> using amber19sb forcefield. All the amino acids are in L- form. I have
> prepared a .pdb file that I can use to generate a .parm7 and a .crd file
> for this cyclic peptide. However, the CMAP entries are missing for the
> terminal residues. Based on Amber20 manual, I have noticed that CMAP will
> not be applied to terminal residues. I can circumvent this issue by
> manually modifying .parm7 file. I would love to know if there is a way to
> force tleap to assign CMAP to "terminal" residues of cyclic peptide?
>
> Thank you
> Minh
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Received on Mon Feb 20 2023 - 08:30:02 PST
