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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Received on Tue Dec 05 2017 - 23:00:02 PST
