Re: restraining parts of a molecule

From: JC Gumbart (
Date: Sun Mar 04 2007 - 22:31:47 CST

I think it's more a question of if res.pdb has the same (or similar)
coordinates to whatever coordinates you are loading (either the pdb
or restart.coor file). The restrained_res.pdb is only used in this
case to read the force constant, NOT for coordinates.

My guess would be the coordinate file you're loading and the
coordinates in the restraint file are significantly different.

On Mar 4, 2007, at 10:20 PM, Stern, Julie wrote:

> Hello,
> I'm having some problems with applying a harmonic force
> constant to restrain parts
> of a protein. I tried a force constant of 5 and one of .5 and it
> has the same effect. It
> blows half the molecule right out of the water shell as a result of
> the minimization step,
> keeping a really long bond between the two parts of the molecule
> and an empty space
> where that part of the molecule was.
> Here is the code excerpt:
> # restraints
> constraints on
> consexp 2
> consref res.pdb
> conskfile restrained_res.pdb
> conskcol O
> Does anyone have any suggestions of what the force constant should
> be or what
> else I can check? Any ideas on why this might be happening? I
> doubled checked that the
> res.pdb and restrained_res.pdb have the same coordinates to start
> with so nothing is
> offset to begin with.
> Thanks.
> --Julie

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