That usually means you have a bonding issue. You will often need to
make little edits to your PDB file and/or leap commands to get carbs
to be loaded properly.
Did you download the amber-style pdb file? Can you send me your pdb file?
On Fri, Apr 17, 2020 at 1:59 AM Pinky Mazumder <pmazumder67.gmail.com> wrote:
>
> Hi Lachele,
>
> Thank you for your reply.
>
>
> I have build the hemicellulose using glycam carbohydrate builder and then I
> am trying to load the pdb file of ''hemicellulose'' using loadpdb command
> in xleap.
>
> But, It shows the error !FATAL: Message: Atom named C1 from 4LA did not
> match !
>
> Attached is the screenshot.
>
> Do you have any idea why this is happening?
>
> Any help would be appreciated.
>
>
> Thank you again.
>
>
> Sincerely,
> Pinky
>
> On Thu, Apr 16, 2020 at 3:23 AM Lachele Foley <lf.list.gmail.com> wrote:
>
> > I usually use tleap rather than xleap, but you should be able to use
> > either. See my previous reply, but also consider the 'combine'
> > command.
> >
> > Learning to use xleap or tleap takes a little time, but the Amber
> > manual does a pretty good job of describing the functions.
> >
> > On Wed, Apr 15, 2020 at 11:14 PM Pinky Mazumder <pmazumder67.gmail.com>
> > wrote:
> > >
> > > Dear Amber Users,
> > >
> > > I have built cellulose chain using xleap command. On the other hand,
> > > I have made the chain of hemicellulose using GLYCAM_06 carbohydrate
> > builder.
> > >
> > > Now, I need to put the chain close together.
> > >
> > >
> > > So, my question is, how can I make the both chains closer together?
> > Should
> > > I load the chain of hemicellulose in xleap? If it is, then what is the
> > > command for this job?
> > >
> > >
> > > Any help would be appreciated. Please forgive me if I am asking something
> > > silly.
> > >
> > > Thank you.
> > >
> > > --
> > > Pinky
> > > AL,US
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Pinky
> AL,US
> _______________________________________________
> 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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AMBER mailing list
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Received on Thu Apr 16 2020 - 23:30:01 PDT
