Thank You. I got it. But I need to ask that is there any tutorial or any
material available from that I can get an idea how to rename the residue,
specially the linkage part?
On Wed, Dec 6, 2017 at 10:45 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Compare the atom names in your pdb with those in the WYB definition,
> maybe 'desc WYB.1' or something. They should agree.
>
> Bill
>
>
> On 12/5/17 8:56 PM, Rajarshi Roy wrote:
> > Dear all,
> >
> > I am trying to simulate protein glycan complex. For that reason I
> extracted
> > my glycan from the pdb file , rename it according to GLYCAM, but when I
> > loaded that pdb in Leap, I am getting some error because of atom naming
> and
> > cannot generate the topology file.I also did pdb4amber but still my issue
> > is there.
> > This is showing in my terminal after loading the pdb file.
> > ------------------------------------------------------------
> --------------------
> > Loading PDB file: ./x.pdb
> > Created a new atom named: C7 within residue: .R<WYB 3>
> > Created a new atom named: C8 within residue: .R<WYB 3>
> > Created a new atom named: O within residue: .R<WYB 3>
> > Created a new atom named: O7 within residue: .R<WYB 3>
> > Created a new atom named: O1L within residue: .R<WYB 3>
> > Added missing heavy atom: .R<WYB 3>.A<C2N 20>
> > Added missing heavy atom: .R<WYB 3>.A<O2N 21>
> > Added missing heavy atom: .R<WYB 3>.A<CME 22>
> > Added missing heavy atom: .R<WYB 3>.A<O5 3>
> > total atoms in file: 46
> > Leap added 48 missing atoms according to residue templates:
> > 4 Heavy
> > 44 H / lone pairs
> > The file contained 5 atoms not in residue templates
> > How do I solve this issue ?
> > I have also attached my pdb file below.
> >
> > Thank you in advance!
> >
> >
> >
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>
--
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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Received on Tue Dec 05 2017 - 22:30:03 PST
