AMBER Archive (2006)

Subject: AMBER: distance restraints

From: mkseo (seo_at_ualberta.ca)
Date: Mon May 01 2006 - 16:49:21 CDT

Hi Amber users,

I want to use the reaction coordinate as distance between
center-of-mass of protein and center-of-mass of ligand in umbrella
sampling.

To specify two groups using IGR1 and IGR2, the manual (p.122) says a
maximum of 200 atoms are allowed in any group.
The protein has 3668 atoms (247 residues) and ligand has 67 atoms (4
residues) in my case.
Do I need to specify atom numbers or residue numbers in IGR1 and IGR2?

For example of residue number,
igr1= 1 247
igr2= 248 251

or example of atom number,
igr1 = 1, 2, 3, 4, 5,........,3668 (Isn't it too much to put all
atoms here?)
igr2 = 3669, 3670, 2671,.....

Can anyone explain more about this?

Thanks.

Mikyung

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