AMBER Archive (2005)

Subject: Re: AMBER: lib file for nonstandard residue

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Thu Jul 14 2005 - 17:02:35 CDT


So what does childsequence mean? I have seen a much larger number
(>5000) here for other proteins such as the one in Ross Walker's
non-standard residue tutorial. Also the simulation seems to work fine
and DIK would have crazy move if both ends are not connected to the
protein.

Eric
On Jul 14, 2005, at 12:37 PM, Bill Ross wrote:

> More...
>
>>> !entry.DIK.unit.childsequence single int <--- what does this mean?
>>> 2
>>
>> 'single' means single value, vs. 'array'. 'int' means it's an integer.
>
> Also I see that entry.DIK.unit.childsequence = 2 is the same for
> standard residues.
>
>>> !entry.DIK.unit.connect array int <--- this looks good to me.
>>> 43
>>> 61
>
> I notice that the connect0, connect1 atoms are first, last
> (e.g. 1, 30) in the standard residues. Offhand I don't think
> this difference shouldn't matter logically, but maybe it does.
>
> Bill
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