Re: [AMBER] issue regarding GLYCAM and amber FF

From: David A Case <>
Date: Thu, 6 Oct 2016 08:11:03 -0400

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

Beyond that, we need more information: you say that "several" bonds are
missing, but it's impossible to offer advice without more details.


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Received on Thu Oct 06 2016 - 05:30:03 PDT
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