AMBER Archive (2004)

Subject: Re: AMBER: Xleap crash, problem with residue bonding

From: opitz_at_che.udel.edu
Date: Mon Jul 26 2004 - 10:39:51 CDT

('binary' encoding is not supported, stored as-is) I went back and checked the *.lib file after this explanation.
It turns out that this bond was there twice, which probably caused the
crash.
My question is, why was that there?
I used the sequence command to attach the residues, but in the past this
has left me with a number of residues floating apart not being bonded
together. Therefore I used the bond command to bond the residues. Would
that have caused the bond to be in the lib file twice? And why would it
put it there twice if it is already there?
 Thanks.
 
 Armin

==============Original message text===============
On Thu, 22 Jul 2004 17:55:58 EDT Bill Ross wrote:

> 1-4: angle 76 192 duplicates bond ('triangular' bond) or angle
> ('square' bond)
> ...
> So it seems that xleap thinks there are problems with certain angles
> duplicating bonds that form a triangle (I guess).

I think this means there are bonds forming triangles or squares.

1-4 interactions are treated seperately for nb calcs because it
is assumed that bond/angle/torsion terms cover those interactions.
As far as I remember, these cyclical structures are detected when
building excluded atom lists from bond and angle (and dihedral?)
lists.

Bill

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu