Re: [AMBER] PDB file carbohydrates naming problem

From: Lachele Foley <>
Date: Wed, 21 Aug 2019 00:07:18 -0400


You shouldn't use TER cards after the NLNs unless they are actually at
the end of an amino acid chain. They are amino acid (modified), and
don't follow the glycan rules.

Removing hydrogens isn't necessary, but their names need to exactly
match the templates in the force fields. Folks usually prefer to just
remove them rather than rename them all. If any of their positions
are critical, leave those in and make sure the names are right.
Otherwise, it's easier to delete them. Or rename them all if you
prefer to do that.

Your NLN and 0YB atom names need to exactly match the templates as
well. The same hydrogen-naming logic applies, but you must ensure
that the heavy-atom names match.

Do you know how to find the lib and prep files where the templates are
(for naming)?

On Tue, Aug 20, 2019 at 11:49 PM Rui Chen <> wrote:
> By the way, should I remove all the hydrogens before using PDB4AMBER and
> why? Thank you.
> On Tue, Aug 20, 2019 at 9:43 PM Rui Chen <> wrote:
> > Hello,
> >
> > I am preparing a PDB file for running LEaP. Since I add glycans using
> > CHARMM GUI, I rename the glycans to NLN (N-linkages to ASN) according to
> > AMBER manual (LEaP). However, I got error when I run leap. I changed the
> > TER cards, but it still didn't work. I also checked the connections between
> > the carbohydrates and the ASN amino acids using VMD, I couldn't find
> > anything wrong. The leap input file, log file, pdb file (mentioned in leap
> > input file) are attached.
> >
> > Could you please give me some clue about how to solve the problem? Looking
> > forward to hearing from you.
> >
> > Sincerely,
> > Rui
> >
> _______________________________________________
> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Tue Aug 20 2019 - 21:30:01 PDT
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