AMBER Archive (2005)

Subject: Re: AMBER: details of new aminoacid

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 18 2005 - 10:01:20 CST

On Tue, Jan 18, 2005, Gustavo Pierdominici Sottile wrote:

> Hi, I send the details of the problems with the developing of a new
> aminoacid. Suppose I have to designate a new amino acid. I create the
> archive .in that looks like this (it is not complete)

The connectivity is determined by the "chain" designations (M,E,S,3,B) in the
fourth column of your input. Use the "edit" command in xleap to look at
your amino acid, and you can see which bonds are there. Since you sent only
a part of your amino acid, it is not possible for me to see why leap thinks
you have a CW-C bond.

>
> WARNING: There is a bond of 3.464102 angstroms between:
> ------- .R<WAT 7341>.A<H2 2> and .R<WAT 7341>.A<O 3>
>
> This is not true because all the bonds in water molecule are smaller then 1
> angstroms.

Use the "desc" command in leap to look at the coordinates of water 7341.
Either there really is a long bond, or the program is not getting the
coordinates you want it to get.

...good luck...dac

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