AMBER Archive (2003)

Subject: Re: Proper Restraint usage

From: CUI, Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Tue Apr 15 2003 - 16:30:22 CDT

Hi,
    You could use nmropt option to just restrain that distance. The
    usage is described in the manual.

On Tue, 15 Apr 2003, Steve Seibold wrote:

>
> Hello
> I am confused about what type of restraint I should use in AMBER. I have
> a heme cofactor bound through the iron to a nitrogen on the proximal
> histidine. When Leap processes the pdb they are not covalently linked
> and during MD they separate. That is, the bond length between iron and
> nitrogen reaches up to 3.0 angstroms.
> I have been able to use position restraints on the iron of the heme and
> nitrogen of the proximal histidine using the NTR = 1 variable and
> defining atom types in the input files. This is keeping the distance
> between the two atoms close so far now. But this is really a position
> restraint of the separate atom's xyz coordinates and not a distances
> restraint between the two atoms.Right?
>
> Am I enforcing the restraint correctly? Should I be using &rst?
>
> Thanks, Steve
>
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-- 
Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790