AMBER Archive (2007)

Subject: Re: AMBER: Restraints on modified NA's

From: David A. Case (case_at_scripps.edu)
Date: Mon Mar 05 2007 - 10:44:56 CST

On Fri, Mar 02, 2007, Seth Lilavivat wrote:
>
> I am attempting to run some explicitly solvated MD runs on modified NA's with
> restraints such as NOE distance and WC distance. I have two questions:
>
> 1. I would like to apply the restaints at the very beginning of the MD run,
> so what pdb file would I have to give makeDIST_RST?

A pdb file that corresponds to your staring coordinates (e.g. use ambpdb on
the prmcrd file made by LEaP.)

>
> 2. Would I have to modify map.DG-AMBER for my custom residues?

Yes. (Assuming you have constraints to the modified residues.)

...dac

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