There is no limit, but if the overall system size becomes too large,
there might be trouble.

Several of us have varying obligations this week, so we can't be fast,
but we are looking into the issue.

You could try doing the first five and then the last two as separate
jobs.  Then, with some work, you could add the last two to the first
system. This is possible because we do not alter the coordinate space
of the protein significantly.  You might need to manually rotate some
bonds if there are clashes.  Also, definitely check the orientation of
the protein side-chain at the attachment points.  If you have no idea
how to do what I just said, let me know.  Folks have done this before
on large systems.

On Tue, Oct 31, 2023 at 2:43 PM Natesan Mani
<[log in to unmask]> wrote:
>
> Hello,
> I did some testing from my end, and it seems like adding more than 5 glycans to my system is giving me the aforementioned error. I have a total of 7 glycans in my system. The glycoprotein builder works perfectly when there are 5 glycans added but adding more than 5 is giving me the error. I am not sure if glycam has a limit on how many glycans can be added. Please let me know !
> ________________________________
> From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Lachele Foley <[log in to unmask]>
> Sent: Monday, October 30, 2023 10:08 AM
> To: [log in to unmask] <[log in to unmask]>
> Subject: Re: Regarding Glycoprotein builder
>
> Thanks.  We will check into this and get back to you.
>
> On Mon, Oct 30, 2023 at 9:54 AM Natesan Mani
> <[log in to unmask]> wrote:
> >
> > The job just completed, and I forwarded the email to you. I also got this error when I submitted the job: "java.io.FileNotFoundException: /website/dev.glycam/userdata/tools/mdfiles/a2g0f_m5_172098d6-79e2-4f17-92ad-1f4ec755d624/stderr_file (No such file or directory)". I refreshed the page and the job was completed.
> > Best,
> > Natesan.
> >
> > ________________________________
> > From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Lachele Foley <[log in to unmask]>
> > Sent: Monday, October 30, 2023 9:50 AM
> > To: [log in to unmask] <[log in to unmask]>
> > Subject: Re: Regarding Glycoprotein builder
> >
> > When you get the email saying that your project is complete, please
> > forward it to [log in to unmask]
> >
> > If you do not receive an email in 24 hours, let me know.
> >
> > On Mon, Oct 30, 2023 at 9:48 AM Natesan Mani
> > <[log in to unmask]> wrote:
> > >
> > > Hello,
> > > Thanks for your reply. The email address I used is [log in to unmask] I currently have assigned a project which is running now, the name of the project is a2g0f_m5.
> > > Best,
> > > Natesan.
> > >
> > > ________________________________
> > > From: Users of GLYCAM & GLYCAM-Web <[log in to unmask]> on behalf of Lachele Foley <[log in to unmask]>
> > > Sent: Monday, October 30, 2023 3:09 AM
> > > To: [log in to unmask] <[log in to unmask]>
> > > Subject: Re: Regarding Glycoprotein builder
> > >
> > > Hi there!  Thanks for contacting us.
> > >
> > > It would help if you could share some more information about your
> > > project.  Did you enter an email address?  DId you get a notice that
> > > your project had completed? If not, do you mind doing that? If you can
> > > forward the email to me ([log in to unmask]), I will be better able to
> > > figure out what happened. Otherwise, if you assigned the project a
> > > name, tell me the name.  Thanks!
> > >
> > >
> > > On Fri, Oct 27, 2023 at 12:00 PM Natesan Mani
> > > <[log in to unmask]> wrote:
> > > >
> > > > Hello everyone,
> > > > I was trying to build a glycoprotein on GLYCAMM. I was able to construct all the necessary glcyans and also found the glycosylation sites to be active. However, when I download the file, there are no glycans on it and I only get the pdf files, I also need the prmtop and inpcrd files. I saw that another user had the same issue. Could you please help me in solving this!
> > > > Best,
> > > > Natesan.
> > > >
> > > >
> > > >
> > > > Natesan Mani
> > > >
> > > > (pronouns: he/him)
> > > >
> > > > PhD student,
> > > >
> > > > Department of Chemical Engineering,
> > > >
> > > > Northeastern University.
> > > >
> > > > Phone: +17134017811
> > > >
> > > > Email : [log in to unmask]
> > > >
> > > > LinkedIn | Website
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA