AMBER Archive (2009)

Subject: Re: [AMBER] thioglycoside

From: FyD (
Date: Mon Jan 26 2009 - 09:07:37 CST

Dear Alexander,

> I want to make a cysteine which has an S-link to a mannose. If I take
> CYM, protect the N and C-function and then set the S-atom to tail and
> connect this to 1MA I can't save my top and crd. I also tried to make
> the molecule with antechamber but again, I couldn't save the top and
> crd files. Does anybody has an idea or experience with this problem?

I think you could follow the strategy reported @
I would even vote for the second strategy, i. e. building a new Cys
residue as well...

regards, Francois

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