Did you load the glycam amino acid libraries? It doesn't hurt to delete
any hydrogens nearby, as Bill suggests.
If you still have trouble, post your leap script here and/or send it to me
separately with the PDB.
On Wed, Nov 23, 2016 at 5:59 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Is loading a modified pdb involved? If so, when you changed the residue
> type, maybe you should have deleted the HD22 atoms before loading pdb?
> Not sure, since I haven't used glycos myself.
>
> Bill
>
>
> On 11/23/16 2:39 AM, Fabrício Bracht wrote:
> > Hi. Sorry for the second email, but I checked the list more thoroughly
> and
> > found a suggestion to change the ASN to NLN, which would have the correct
> > charge. But changing the ASN residues that link to glycosidic residues
> made
> > tleap create HD22 atoms for all of them and then, when I check the unit,
> it
> > states that HD22 does not have a type.
> > Thank you
> > Fabrício
> >
> > 2016-11-23 8:26 GMT-02:00 Fabrício Bracht <fabracht1.gmail.com>:
> >
> >> Hi. I submitted a structure to the Glycoprotein builder in GLYCAM and
> when
> >> going through tleap, I got the error saying that the total charge
> >> (-46.0300000) is not integral.
> >> I used leaprc.protein.ff14SB and leaprc.GLYCAM_06j-1 and the protein
> file
> >> directly from the server.
> >> Any idea why this happened?
> >> Thanks
> >> Fabrício
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> _______________________________________________
> 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 Wed Nov 23 2016 - 03:30:03 PST
