Re: AMBER: Antechamber/formatting question

From: FyD <>
Date: Mon, 28 Feb 2005 05:12:37 +0100

Quoting Kara Di Giorgio <>:

> I have a pdb of the modified guanine. My problem is the "caps". I
> have charges and everything else for the modified guanine. How do I
> handle removing the "cap"? When I load the DNA and my modified residue
> into xLeap, it keeps the cap atoms. If I delete them, it tells me that
> there is no longer an integral charge, etc. What should I do?

You need to use intra-molecular (IMR) restraints in resp. I would say:
1- run R.E.D. without IMR
2- use the espot file and modify the resp input1/2 to add these IMR amd re-run

All this has been already discussed several times and is available in the R.E.D.
FAQ. This will be done automatically with R.E.D.III...


  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
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Received on Mon Feb 28 2005 - 04:53:00 PST
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