Found a solution. I was using the protein file with hydrogens that came
from the glycoprotein builder. I renamed the ASN residues manually and then
removed the hydrogens with pdb4amber. I had tried this before but hadn't
used pdb4amber. Using it made things work alright.
Thank you
Fabrício
2016-11-23 9:01 GMT-02:00 Lachele Foley <lf.list.gmail.com>:
> 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
> > >>
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> > >
> >
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
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Received on Wed Nov 23 2016 - 03:30:03 PST
