You can add ions and solvate on the site.
Can you share the PDB file you got from our site? Specifically, send
the one you are using with tleap. If you don't want to share it on a
mailing list, you can send it to me personally.
On Fri, Jan 3, 2020 at 6:43 PM zz sheng <shengzizhang.gmail.com> wrote:
>
> Hi Lachele,
>
> The structure files I downloaded from Glycam are the Amber format, they didn't have Asn
> changed to NLN. I am curious about this too. That is one of the reasons the MD will give errors too if using the downloaded files for input to Amber.
> The second reason I regenerate the topo files is that I want to add ions to neutralize the charge.
>
>
> Best,
>
> Zizhang
>
> ________________________________
> From: Lachele Foley <lf.list.gmail.com>
> Sent: Friday, January 3, 2020 5:44:14 PM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Glycosylation issue: Atom xx was assigned a lower molecule # than previous atom.
>
> If you used our website to add Man3, then why not use the files
> provided there? I am confused that you needed to change the ASN
> residue to NLN. That should already have been done. Can you provide
> more details?
>
> Basically... I think you are doing more work than you need to do, and
> that is confusing things.
>
> On Fri, Jan 3, 2020 at 4:44 PM zizhang sheng <shengzizhang.gmail.com> wrote:
> >
> > Hi All,
> > I used Glycam website to add an MAN3 to my protein. I then renamed the ASN residue to NLN, and used teleap to generate topology and coordinate files. While teleap did not report any error, AMBER continue to report an error during MD (heating, equilibration, production): atom was assigned a lower molecule # than previous atom. If manually checking the structure, the atoms were assigned correctly. The atom in trouble is the C1 atom of 4YB. I attached the PDB files for teleap, the teleap script, and the generated top files. If using ambpdb to convert the topology file to pdb format, the same error occurs. But if I run MD on the protein without glycosylation, the MD run is good.
> > Hope you can help me figure out why this happens.
> >
> > Thanks,
> >
> > Zizhang Sheng
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Fri Jan 03 2020 - 16:00:02 PST
