AMBER Archive (2004)

Subject: Re: AMBER: restraint

From: David A. Case (
Date: Tue Jan 20 2004 - 17:05:59 CST

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 | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to