Quite likely, in which case 'desc ACE' will show the same atom names as
were created. If my interpretation were right, you'd be unable to
saveamberparm in leap because of untyped/misnamed atoms.
On 12/20/18 2:44 AM, David Cerutti wrote:
> My take is that is just tleap doing what it needs to complete the residue.
> It was missing some hydrogens. If you had different names for those same
> hydrogens, modify your input structure.
>
> Dave
>
> On Thu, Dec 20, 2018, 3:40 AM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> Either use atomNameMap entries in leap to map to the Amber atom names,
>> or modify your pdb to match. 'desc ACE' in leap to see what the gods
>> want of you. :-)
>>
>> On 12/20/18 12:22 AM, Keiran Corbett wrote:
>>> Hello,
>>>
>>> I keep getting errors of this kind in tleap and wondered what peoples fix
>>> was if this has happened
>>>
>>> AmberTools18
>>>
>>> Created a new atom named: HH31 within residue: .R<ACE 111>
>>> Created a new atom named: HH32 within residue: .R<ACE 111>
>>> Created a new atom named: HH33 within residue: .R<ACE 111>
>>> Created a new atom named: HH31 within residue: .R<ACE 123>
>>> Created a new atom named: HH32 within residue: .R<ACE 123>
>>> Created a new atom named: HH33 within residue: .R<ACE 123>
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>>>
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Received on Thu Dec 20 2018 - 03:30:02 PST
