AMBER Archive (2006)

Subject: AMBER: ibelly & fix atom

From: rdauria_at_uci.edu
Date: Mon Apr 17 2006 - 22:41:28 CDT

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.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu