[AMBER] cyclic peptide in water box

From: Sepideh Jafari via AMBER <amber.ambermd.org>
Date: Mon, 13 Nov 2023 09:29:35 +0100

Dear Amber user,

Iam writing to kindly ask if someone has the same problem as mine..
I am trying to simulate cyclic peptide (PFPF) in water boxes, DMSO, and
Unfortunately, especially for water after some ns, in cpptraj I get this
error (Too many iterations in routine! Convergence failed) and the graph
deformed. U can find in the attachment this graph of RMSD. and (also my
computer crashed and I should forced the pc to shut down)
both for the dmso and mccn box, it is fine.
and another issue. I have 2 confirmations of my cyclic peptides.PFP(D)F/
PFP(L)F one phenylalanine in D- one in L- form. I think after tleap the D
one changed to L conformation.
I don't know how to fix this.

I would be grateful if you could share your experience with me. Thank you
so much.

Kind regards.
Sepideh Jafari

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(image/png attachment: rmsd-deformed.png)

Received on Mon Nov 13 2023 - 01:00:02 PST
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