Re: AMBER: AMBER 8: Freeze AND restrain questions

From: Viktor Hornak <hornak.csb.sunysb.edu>
Date: Mon, 24 Jan 2005 13:02:53 -0500

Dear Guillaume,

I don't think you can mix an older "GROUP" input with new restraintmask
option. Also, I would use dihedral restraints (see chap. 5.9 in amber8
manual) for freezing internal coordinates of your substrate.
Furthermore, I'd use positional restraints (ntr=1, ibelly=0) and not
belly for the region you want to restraint. The way I understood it,
you'd probably want this selection for the restrained region:
restraintmask=':442>:8.0' (don't forget to apply bugfixes for amber8,
especially bugfix.7 that deals with atom selections based on distance).
You might want to post your input file once you think you put in all the
changes suggested above...

-Viktor


Guillaume Bollot wrote:

> 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
> e-mail: Guillaume.Bollot.chiorg.unige.ch
>
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Received on Mon Jan 24 2005 - 18:53:00 PST
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