AMBER Archive (2005)

Subject: Re: AMBER: unnatural ligand

From: Eric Hu (yhu_2003_at_yahoo.com)
Date: Mon Feb 07 2005 - 12:28:14 CST

I can see that the unnatural residue connects with the
two neighbor amino acids in xleap-->edit. When I
reload the lib file after seting head and tail, desc
shows that head is NULL. When I work on Ross Walker's
tutorials, the same thing happens again.

Eric
--- "David A. Case" <case_at_scripps.edu> wrote:

> On Thu, Feb 03, 2005, Eric Hu wrote:
>
> > Hi, I made frcmod and lib files for an unnatural
> > residue called LIG(covalently bonded with lys).
> leap
> > can write the top and crd sucessfully showing that
> LIG
> > joins with two neighbouring a.a.
>
> Can you be more specific? What did you take as a
> "successful showing that LIG
> joins with two neighboring a.a."?
>
> > There is a "Ter"
> > between the C-terminal of the unnatural residue
> and
> > the next a.a. in the new pdb
>
> This suggests that the two amino acids are in fact
> not bonded -- hence my
> first question.
>
> ...dac
>
>
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