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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Received on Tue Dec 05 2017 - 21:30:02 PST
