[gmx-users] Choosing terminals with AMBER ff

[Justin Lemkul]

On 11/8/17 6:25 AM, Simon Kit Sang Chu wrote:
> Dear Mark,
>
> Thank you very much. I am worried with the ends attracting each other for a
> long peptide. May I ask for the general strategy simulating segments of a
> protein? I believe simulating part of the whole protein might not be
> something new.

You have to do like Mark suggested and manually build an ACE cap on the 
N-terminus if you want it to be uncharged. There are also NME/NHE 
termini for the C-terminus to be modeled as an amide. Indeed, this isn't 
a new concept. But AMBER defaults to assuming specific N- and C-terminal 
versions of their amino acids. The user has to go the extra step of 
building proper termini and naming them as such. All force fields 
support capping groups, and they are routinely used, but some force 
fields are easier to deal with via normal .n.tdb and .c.tdb entries.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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