AMBER Archive (2009)

Subject: Re: [AMBER] Load protein complex to Xleap (Combine)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sat Mar 28 2009 - 16:39:35 CDT

On Sat, Mar 28, 2009, Rilei Yu wrote:
>  
> I want to perform MD on my protein complex which consits an organic
> molecue and a receptor. As there is no field paremeters for this organic
> molecue, I used ANTECHAMBER to obtain the org.prepin and org.frcmod
> files. Then I obtained the ptomtop and inpcrd successfully, but I still
> have some problems. After load org and receptor to xleap I find the org
> (Ligand) was not in the binding cavity.

This is to be expected: the coordinates in the prep file are not those
from the complex.

> (I can load the complex accurately by loading  the procomplex directly,
> but now I want to load the receptor and ligand respectively!)

It's not clear why you want to load the two separately. But if you do,
edit the complex file to create separate pdb files (receptor and ligand),
then use two loadpdb commands to bring both into leap -- that way you will
get the coordinates of the complex for both.

...dac

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