Dear Hector,
I hope this email finds you well.
First and foremost, I would like to express my appreciation for your assistance. Your guidance has been invaluable to my work, and I'm truly grateful for it.
I've been encountering a specific issue while using software and web servers like the 3xDNA web server, and I believe your expertise might help shed some light on it. Specifically, when attempting to save the constructed DNA as a PDB file and subsequently applying the Amber force field using pdb2gmx in Gromacs, I'm encountering the following error message:
"Atom P in residue DA 1 was not found in rtp entry DA5 with 30 atoms while sorting atoms."
To address this issue, I manually delete the first phosphate and its attached oxygen atom, which does allow me to successfully run pdb2gmx with the Amber force field. However, I'm curious if there are alternative approaches or recommendations you could provide to resolve this issue more efficiently or effectively.
Your insights into this matter would be greatly appreciated. Once again, thank you for your support, and I look forward to your response.
Best regards,
fatemeh,
On Saturday, September 30, 2023 15:45 CEST, "Hector A. Baldoni via AMBER" <amber.ambermd.org> wrote:
Dear Amber users,
To build circular DNAs you would use the following server:
https://mmb.irbbarcelona.org/MCDNA/
To design three-dimensional DNA origami I suggest:
https://cadnano.org/
https://cando-dna-origami.org/
https://yanlab.asu.edu/Resources.html
Greeting,
Hector
El 2023-09-30 08:07, Fadaei Fatemeh Mgr. via AMBER escribió:
> For constructing straight DNA, I have tested Chimera and saved the
> output PDB file for Amber. It was compatible with Amber and pdb2gmx.
> However, when it comes to modifying the DNA and creating circular DNA
> structures, I'm still looking for a solution. I would be grateful if
> anyone has any suggestions.
>
> On Thursday, September 21, 2023 04:35 CEST, David A Case via AMBER
> <amber.ambermd.org> wrote:
> On Wed, Sep 20, 2023, Claire Harmange Magnani via AMBER wrote:
>>
>> Other than attempting to download an older version of Ambertools, what
>> other options do I have to build and modify DNA structures so that
>> they
>> will be compatible with Amber?
>
> "Compatibility with Amber" is the least of your problems. Any software
> that
> can create a PDB-format set of coordinates should work. It helps if
> that
> software uses IUPAC/PDB nomenclature, since that is what Amber uses.
> But
> it's usually pretty trivial to convert some set of atom names to the
> standard.
>
>> I had hoped to familiarize myself with Amber by following this
>> tutorial
>> <https://ambermd.org/tutorials/basic/tutorial1/>
>
> That tutorial is fine, but note that (as with all MD runs) one needs a
> starting conformation. NAB is one way to generate those, but plenty of
> other pieces of software can also do this. (A *lot* depends on what
> sort of
> DNA structures you have in mind, so it's hard to be more specific.)
>
>> <https://bionano.physics.illinois.edu/sites/default/files/x3dnatutorial_0.pdf>.
>
> Note that this seems to be exclusively aimed at double-stranded DNA
> (perhaps
> with modified nucleotides.) Creating model of double-stranded DNA is
> pretty
> easy, even in Amber. Althought the NAB program for this (used in the
> old
> tutorial) is no longer present, the fd_helix program is still there, in
> nabc. So if you interest is in double-stranded DNA, just play around a
> bit.
>
> ....dac
>
>
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--
--------------------------------------
Dr. Hector A. Baldoni
Profesor Titular (FQByF-UNSL)
Investigador Adjunto (IMASL-CONICET)
Area de Quimica General e Inorganica
Universidad Nacional de San Luis
Chacabuco 917 (D5700BWS)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
I do not define time, space, place, and motion, as being well known to
all.
-- Newton (1642-1726), Principia
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Received on Sat Sep 30 2023 - 09:00:02 PDT
