More interpretation: 'default_name' implies its your own residue.
Missing connect1 would be the 'tail' atom of the first of the two
residues, so ATP connect1 most likely.
Bill
On 10/16/16 1:42 PM, Bill Ross wrote:
> It looks like you need to make LIG 1 atom CD2 a connect[0/1] atom in
> your residue template for LIG. I can't find any web pages for it, so
> checking the manual would be in order.
>
> Bill
>
>
> On 10/16/16 1:09 PM, Paul Meister wrote:
>> Hello,
>>
>> I'm trying to build my topology and coordinate files for my enzyme so I can
>> begin my MD, but I get an error during LEaP which I'm not sure how to
>> solve. I have loaded parameters for two different ligands, but I'm not
>> entirely sure what this error is telling me.
>>
>> One sided connection. Residue: default_name missing connect1 atom.
>> ERROR: Comparing atoms
>> .R<ATP 390>.A<O3B 7>,
>> .R<ATP 390>.A<O1G 9>,
>> .R<ATP 390>.A<O2G 10>, and
>> .R<ATP 390>.A<O3G 12>
>> to atoms
>> .R<ATP 390>.A<O3B 7>,
>> .R<LIG 1>.A<CD2 1>,
>> .R<ATP 390>.A<O1G 9>, and
>> .R<ATP 390>.A<O2G 10>
>> This error may be due to faulty Connection atoms.
>> !FATAL ERROR----------------------------------------
>> !FATAL: In file [chirality.c], line 142
>> !FATAL: Message: Atom named CD2 from LIG did not match !
>>
>> Everything before this was running fine. I have also done this same process
>> before for another enzyme, but I haven't seen this error. Is there some
>> kind of issue with the ATP parameters? I have uploaded the prep file and
>> frcmod file for ATP.
>>
>> Thank you,
>>
>> Paul Meister
>>
>>
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Received on Sun Oct 16 2016 - 16:30:02 PDT
