AMBER Archive (2004)

Subject: RE: AMBER: Amber force field for protein-DNA system

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jun 01 2004 - 13:09:37 CDT

Dear Jeny,

You may want to take a look at the Amber 8 DNA tutorial
http://amber.scripps.edu/tutorial/polyA-polyT_New/index.html

This covers editing a pdb file to make it suitable for LEaP and then loading
the relevant parameter files into leap for modelling a 10-mer of DNA.
Although the tutorial only covers DNA the set up information for LEaP loads
both the protein and nucleic acid data files and so it should be suitable
for modelling a protein-DNA system.

I hope this helps
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |
 

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of jz7_at_duke.edu
> Sent: 01 June 2004 09:14
> To: amber_at_scripps.edu
> Subject: AMBER: Amber force field for protein-DNA system
>
> Dear all,
>
> I am new to the Amber force field. I am wondering which
> parameter file I
> should use for a protein-DNA system? I saw parameters for protein and
> nucleic acid seperately. But is there a parameter file for both?
>
> Thanks a lot!
>
> Best,
> Jeny
>
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