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!
--
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
India
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- chemical/x-pdb attachment: x.pdb
Received on Tue Dec 05 2017 - 21:00:02 PST
