From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Wed Nov 28 2007 - 10:30:15 CST
Dear Xavier,
As far as I know, acetylating and methylating your ends would be the
best option to obtained uncharged ends. So far it has worked for me.
Cheers,
Michel
2007/11/28, Xavier GALLET <xgallet_at_nautilusbiotech.com>:
> Dear NAMD users,
>
> I'm using NAMD to analyze MD trajectories of a homodimer protein connected
> by disulfides bridges.
> I'd like to get uncharged terminal ends in my protein (NH2- and -COOH
> termini). I already looked at the mailing list and the charmm topology file,
> but it seems that the only way is to put acetylated N-end and methylated
> C-end by using :
>
> first ACE
> last CT1
>
> I also tested :
>
> first NONE
> last NONE
>
> but the N- and C-ends are converted into NH- and -CO, respectively.
>
> So, can you confirm to me that the unique solution is to use ACE/CT1 for
> uncharged ends ?
>
> Thanks in advance,
>
> Xavier
>
>
>
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