That was the issue, I believe.
https://listserv.uga.edu/cgi-bin/wa?A2=ind1610&L=GLYCAM-L&D=0&P=2787
(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 <david.case.rutgers.edu> 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
>
>
> _______________________________________________
> 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
Received on Thu Oct 06 2016 - 09:00:02 PDT
