AMBER Archive (2007)

Subject: Re: AMBER: LEaP bond problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Nov 07 2007 - 10:39:49 CST

On Wed, Nov 07, 2007, Beale, John wrote:

> I have a protein with a serine at the active site. The serine is residue
> 53 and the ser-OH is designated OG. I want to bind the serine-OG to the
> phosphorus of a phosphonate ligand. The ligand is residue 500 and the
> phosphorus is designated P. I would like to bond OG to P. In xleap I
> enter "bond blh.53.OG blh.500.P". I am getting an error message that
> states:
>
> bond: Argument #2 is type String must be if type: [atom]
> usage: bond <atom1> <atom2> [order]
>

This means that the second atom is not recognized as an atom, so LEaP thinks
it must be a string. Use the desc command in LEaP to figure out what your
phosphorus atom really is -- my best guess is that the residue is no longer
numbered 500, but is now something different.

However: this is probably not enough, since you will need to remove the HG
atom (I presume), also get the charges and other force field parameters.
The usual procedure would be to create a new residue, serine + ligand. Take
a look at how phosphoserine is constructed in the "contributed parameters"
database...this might get you started in the right direction.

...good luck...dac

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