Hi!
The atom definitions are in the prep file. Since you know you want WYB, I
presume you understand basic glycam residue naming. If you look for the
WYB entry in the prep file, you should be able to figure out the naming
translation pretty easily, but do ask if you have trouble.
prep file:
http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/03/GLYCAM_06j-1.prep
Do you need the geometry already in the pdb file you have, or do you just
need a build of the glycan?
On Wed, Dec 6, 2017 at 1:32 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> I'm not sure what you mean, e.g. sometimes I copy a file and edit it
> before loading in leap.
>
> But the tutorials are worth skimming to see what applies to you, and
> could save embarrassment.
>
>
> On 12/5/17 10:14 PM, Rajarshi Roy wrote:
> > 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Dec 07 2017 - 19:30:02 PST
