Re: [AMBER] cyclic peptide in water box

From: Dr. Anselm Horn via AMBER <>
Date: Mon, 13 Nov 2023 10:05:39 +0100


concerning your two issues:

1, minimization
Maybe your system is too strained initially (e.g. because your input
geometry does not reflect the peptide bond reflecting the cyclic peptide
structure, but it's hard to tell without knowing more details).

A normal piece of advice would be to print out the structure at every
simulation step, so you can visualize the course of that minimization
and perhaps see, what's going wrong. Maybe you can use a less-strained
input structure.

2, D-/L-peptide
A D-configuration of a residue read-in from an external file is not
changed by tleap. If you, however, only have the backbone atoms present
in your input structure, tleap will add the side chain (i.e. the missing
atoms) in L-configuration, since this is the structure stored in the
parameter data base.

Maybe this helps.

Good luck,


Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)

Am 13.11.2023 um 09:29 schrieb Sepideh Jafari via AMBER:
> Dear Amber user,
> Hello,
> 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
> MeCN.
> 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
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Mon Nov 13 2023 - 01:30:03 PST
Custom Search