AMBER Archive (2006)

Subject: RE: AMBER: ibelly & fix atom

From: Ross Walker (
Date: Mon Apr 17 2006 - 23:08:42 CDT

Dear Raffaella,

> move. Since I do not want to use a harmonic restraint but
> plainly fix the
> O I think I should use ibelly=1. Is that correct?

This is correct, just be aware of the issues that involve using belly. I.e.
pressure calculations are innacurate, temperature control is not strictly
correct etc.
> ibelly = 1,
> ibellymask='!@OH',

This should be bellymask, NOT ibellymask.

Also, do you only have one atom with name OH? If you do then the above is
fine. However, if you have more than one atom with name OH be aware that all
atoms of name OH will be frozen. In this case it is probably safer to use
the atom number so: @xxx where xxx is the atom number.

Also, be aware that @OH means 'name=OH' if instead you mean type=OH then you
need to use @%OH.

Good luck...


|\oss Walker

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