AMBER: AMBER 8: Freeze AND restrain questions

From: Guillaume Bollot <>
Date: Mon, 24 Jan 2005 17:19:11 +0100

Dear all users,
I would like to know if it's possible to perform minimization and dynamic
with special restraints.
I explain my problem :
I have a protein (wich contain an active site) , a substrat(RES 442) and a
water cap. I want to freeze only the internal coordinates of my substrat(I
used Targeted MD : ITGTMD=1, TGTMDFRC=100.0 with the RES section at the end
of my input file) AND I would like to define moving sphere within 8 angs.
around my substrat (I used AMBMASK for the list of the residues and
IBELLY=1, NTR=1 , RESTRAIN_WT=100.0 and BELLYMASK=":442""<8.0"""":WAT".
My question are :
my syntax is correct?
Is it possible to perform minimization with this kind of restraints?
If not how to do that with AMBER 8?

Thanks very much in advance.

BOLLOT Guillaume
Organic Chemistry Department
University of Geneva
30, quai Ernest-Ansermet
CH-1211 Geneva 4
tel. +41-22 379 6155

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Received on Mon Jan 24 2005 - 16:52:59 PST
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