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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Received on Wed May 03 2006 - 06:07:08 PDT
