Re: AMBER: restraint

From: David A. Case <>
Date: Tue, 20 Jan 2004 15:05:59 -0800

On Tue, Jan 20, 2004, tang kwa wrote:
> I have followed the tutorial MD of DNA in Amber
> homepage. The system contains 10 basepairs, 18 Na+ and
> water molecules. In equilibration step, the solute was
> restrained with 25 kcal/mol/Ang^2 and reduced by 5
> kcal/mol/Ang^2 untill no restraint. As I have seen in
> input file, the restraint was placed on solute (RES 1
> 20). My question is that the restraint was placed on
> only DNA or both DNA and Na+?
> As I understand, it should be placed on residue 1 to
> 20 which means only DNA. But I have read in some
> iteratures that the harmonic restraint was placed on
> DNA and Na+ ions, which made me confuse.

It doesn't make much sense to restrain the Na+ positions: they are supposed
to diffuse around, even during equilibration. You can look in the prmtop
or pdb files to see what the first 20 residues are; in this case, you should
find that that matches the 20 DNA nucleotides, but not the counterions.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Tue Jan 20 2004 - 23:53:01 PST
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