Re: [AMBER] issue regarding GLYCAM and amber FF

From: Lachele Foley <>
Date: Thu, 6 Oct 2016 11:45:07 -0400

That was the issue, I believe.
(sharing link in case someone comes here and wants to see more discussion.

On Thu, Oct 6, 2016 at 8:11 AM, David A Case <> wrote:

> On Thu, Oct 06, 2016, Mahrukh Imtiaz wrote:
> > I am currently trying to perform MD simulations of p-glycoprotein
> > with N-glycans attached to it, but I am having some issues while
> > creating inpcrd and prmtop files via xleap. I have attached glycans via
> > GLYCAM_web but when I load the pdb file into xleap, it shows several
> > missing bonds among the glycan chains including the covalent bond
> > between ASN and GlcNAc. Moreover, when I draw the missing bonds in xleap
> > it gives missing bond, angle and torsion parameter errors. I have been
> > trying to fix this issue but couldn't get any luck. Any help to solve
> > this issue is highly appreciated.
> Did you change the name of the amino acid that is glycosylated from ASN to
> NLN? If not, that would explain the problems with the missing bonds to the
> protein.
> Beyond that, we need more information: you say that "several" bonds are
> missing, but it's impossible to offer advice without more details.
> ....dac
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> AMBER mailing list

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Thu Oct 06 2016 - 09:00:02 PDT
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