Dear David,
I have a follow-up question. I generated a tleap input file (tleap.in) and
a PDB file, I attached both of them here. Tleap doesn't understand the bond
commands. I also attached the log file. I used the same script file,
previously it worked. Could you please help me check what's the problem? I
opened the PDB file in VMD, there is no long bond between ASP or NLN 280
and glycan or 0YB 427. Looking forward to hearing from you. Thank you.
Best regards,
Rui
On Wed, Nov 27, 2019 at 2:58 PM Rui Chen <rchen6.ualberta.ca> wrote:
> Dear David,
>
> I have a follow-up question. I generated a tleap input file (tleap.in)
> and a PDB file, I attached both of them here. Tleap doesn't understand the
> bond commands. I also attached the log file. I used the same script file,
> previously it worked. Could you please help me check what's the problem? I
> opened the PDB file in VMD, there is no long bond between ASP or NLN 280
> and glycan or 0YB 427. Looking forward to hearing from you.
>
> Best regards,
> Rui
>
> On Wed, Nov 27, 2019 at 9:52 AM Rui Chen <rchen6.ualberta.ca> wrote:
>
>> Dear David,
>>
>> Thank you for your reply. Have a nice day.
>>
>> Best regards,
>> Rui
>>
>>
>>
>> On Wed, Nov 27, 2019 at 9:43 AM David A Case <david.case.rutgers.edu>
>> wrote:
>>
>>> On Wed, Nov 27, 2019, Rui Chen wrote:
>>> >
>>> >Thank you for your help, I solved the problem. I have a simple
>>> question, in
>>> >tleap.log file almost for all the residues I can see "(Residue 2: ILE,
>>> >Nonterminal, was not found in name map.)" But in leap itself (from
>>> >terminal), I could not see this sentence. I found in the previous
>>> mailing
>>> >list, people have similar questions. Should I do something or I don't
>>> need
>>> >to worry about this?
>>>
>>> Don't worry about this: we will probably finally remove this message
>>> from the leap.log file with the next release.
>>>
>>> FWIW: "Nonterminal" means that residue 2 is in the middle of the chain,
>>> and is not an N-terminal or C-terminal residue.
>>>
>>> "not found in name map" means that ILE was not renamed to something else
>>> via a PdbResMap entry.
>>>
>>> Neither one of these facts is (generally) of the slightest interest to
>>> anyone. This message was coded in about 1990, when tleap was very new
>>> (so people wanted to follow what is was doing) and proteins being
>>> simulated had maybe a hundred residues. By now, it's just noise that
>>> makes the leap.log file much less helpful to users. The camel's back
>>> for me came when a built a system with about 70,000 residues.
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Wed Nov 27 2019 - 14:30:01 PST
