AMBER Archive (2005)

Subject: Re: AMBER: distance restraints between two centers of mass

From: Fabien Cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Thu May 26 2005 - 04:01:08 CDT

Dear Javier,

I think you should put nmropt=1.
In your input file, you have nmropt=0, so the distance restraint is not
used (see page 94
of the amber8 manual).

Good luck,
Fabien

JAVIER PEREZ wrote:

> Hi amber users,
>
>I'd like to run a minimization using distance restraints. My idea is to fix
>the distance between two centers of mass and then to run the minimization.
>
>I've defined the two centers of mass and the minimization runs but it doesn
>t work correctly. I check the structure of the system and I can see that the
>minimization run without taking into account the distance restraints.
>
>Next, I'll show you the files I've created for that minimization:
>
>minimization.in
>
>&cntrl
> imin=1, nmropt=0,
> ntx=1, irest=0, ntrx=1,
> ntb=1, igb=0, nsnb=25,
> ipol=0, gbsa=0,
> dielc=1.0, cut=8.0, intdiel=1.0,
> scnb=2.0, scee=1.2,
> ibelly=0, ntr=0,
> maxcyc=150
> &end
> &wt type='END' &end
>DISANG=/disk7/xavip/irlandaII/Epotential/dist10.f
>_____________________________
>
>dist10.f
>
>&rst
>iat=-1,-1,
>iresid=1,
>ir6=0,
>r1=0.00,
>r2=10.0,
>r3=10.0,
>r4=50.0,
>rk2=500000.0,
>rk3=500000.0,
>igr1=2,2,3,3,5,8,
>grnam1(1)='C02', grnam1(2)='C05', grnam1(3)='C02', grnam1(4)='C05',
>grnam1(5)='O2', grnam1(6)='O2',
>igr2=1,1,1,1,
>grnam2(1)='NP3', grnam2(2)='C06', grnam2(3)='C13', grnam2(4)='NP6',
>&end
>
>The distance I want to fix is 10 A.
>
>I accept any suggestion.
>
>Thanks in advance
>
>Javier
>
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-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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