uncharged ends

From: Xavier GALLET (xgallet_at_nautilusbiotech.com)
Date: Wed Nov 28 2007 - 09:46:22 CST

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,


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