AMBER Archive (2003)

Subject: Re: CARNAL

From: Lepsa (lepsik_at_marilyn.uochb.cas.cz)
Date: Tue Jan 21 2003 - 12:07:18 CST

ad> distances

I'd better switch to group specification for DISTANCE measurements, as you
used. What didn't work for me was;

 DIST OD1 25 H20
199;
           ATNAME1 RESNUM1 ATNAME2 RESNUM2

> Ad H-bonds) What does it mean when I get different atom order in an H-bond
> like H - O........O ?

> +++ Sorry I do not understand this question. :-( or what you said mean
> H-O...H H-bond which seems stupid!? Are you using amber7 or someother
> version?

The thing is, the majority is written out as they should be, i.e.
donor-Hatom.......acceptor.
Here, the first two atoms are reversed. As well, I didn't get the H-O.....H
notation. Yes, I'm using A7.

Regards,

Martin Lepsik