Re: [AMBER] issue regarding GLYCAM and amber FF

From: Mahrukh Imtiaz <>
Date: Thu, 6 Oct 2016 12:19:11 +0000 (UTC)

Hi David,Yes, I changed the name of ASN to NLN and created the missing bonds among glycan by the bond command. Despite all that, there appears to be some problem with torsion terms as it gives the error of missing torsion terms when I create the parameter file in xleap. I would be grateful if you could guide me through this.

    On Thursday, October 6, 2016 5:11 PM, 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

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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