Re: [AMBER] bond command

From: Jason Swails <>
Date: Thu, 22 Apr 2010 20:52:11 -0400


On Thu, Apr 22, 2010 at 8:31 PM, Siddharth Rastogi <> wrote:

> Dear AMBER users,
> I understand from Amber manual that, the *bond* command in leap can
> generate
> the bond between atom1 and atom2.
> Both of these ATOMs must be contained by the same UNIT. I have a doubt
> here.!!

The UNIT is not limited to a single 'molecule'. For instance, consider the
following commands:

l = sequence {NALA CALA}
k = sequence {NGLY CGLY}

j = combine {l k}

l, k, and j are all units. The following bond cannot be done:

bond k.1.CA l.2.CA

in order to bond the carbon alpha of the first alanine of a dipeptide to the
carbon alpha of the first glycine of a different dipeptide. However, this
can be done with the command:

bond j.1.CA j.3.CA

because j is a UNIT that contains both dipeptides. This is an example to
show what is allowed, and is thoroughly ridiculous to actually employ, but
it illustrates this concept sufficiently in my opinion.

> I have a sugar molecule, which I want to attach to the protein.
> Is it possible to create a bond between one atom of sugar (atom1) and
> another atom from protein (atom2) molecule by using the Leap's bond
> command??

You must make sure that both are in the same unit (see my above example),
but this is quite possible.

> If it is NOT possible through Leap, can anybody suggest how I will generate
> the complex of sugar and protein ?
> Thanks in advance for your kind suggestion.

Good luck!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
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Received on Thu Apr 22 2010 - 18:00:03 PDT
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