AMBER Archive (2006)

Subject: Re: AMBER: ibelly & fix atom

From: rdauria_at_uci.edu
Date: Mon Apr 17 2006 - 22:59:56 CDT

Hello again,

Sorry I had a typo in the &cntrl group (is bellymask and not
ibellymask!!!). However if you have any suggestions on how to fix an atom
within a molecule in a better way please let me know.

Thanks :)

Raffaella.

> Hello All,
>
> I need to fix the position of one atom (O) and let the rest of the system
> 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?
>
> I am using amber 8 and I am also a bit confused on the use of ibellymask.
> I tried the following input file but it does not work (the only atom type
> I want to fix is OH):
>
> &cntrl
> imin = 0,
>
> ntx = 1, irest = 0,
>
> ntpr = 1000, ntwr = 1000, ntwx = 1000,
> iwrap = 0,
>
> ntf = 2, ntb = 0,
> cut = 12, ipol = 0,
>
> nstlim = 1000000, dt = 0.001, t = 0,
>
> ntt = 1, temp0 = 300.0, tautp = 1.0,
>
> ntc = 2, tol = 0.00001,
>
> ibelly = 1,
> ibellymask='!@OH',
> &end
>
> Any idea of what I am doing wrong?
>
> Thanks a lot :)))
>
> Raffaella.
>
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