AMBER Archive (2002)

Subject: Re: targeted MD

From: Peter VARNAI (Peter.Varnai_at_ibpc.fr)
Date: Sat Oct 19 2002 - 09:26:30 CDT

Tageted MD does not read force constant from GROUP
input (check manual) thus the proper input section:
 &cntrl
    itgtmd=1, tgtrmsd=3.04, tgtmdfrc=5.0
 &end
Group input: target
RES 1 124
END

Good luck,
Peter

> ----- Original Message -----
> From: "Giulio Rastelli" <rastelli.giulio_at_unimo.it>
> To: <amber_at_heimdal.compchem.ucsf.edu>
> Sent: Friday, October 18, 2002 10:28 AM
> Subject: targeted MD
>
>
> > Dear all,
> > The following input for a Targeted MD produced a memory faulf, a core,
> > and just
> > the beginning of an output, with no informative message.
> > I am using Targeted MD to convert two conformations of a molecule, using
> > gbsa.
> > The initial conformer has a rms of 3.04 compared to the reference
> > structure.
> > Any hints? Thank you very much
> > Giulio
> >

> > input:
> > Targeted MD
> > &cntrl
> > nmropt=1,
> > imin=0, nstlim=50000, dt=0.001, temp0=300.0, ntt=1,
> > ntx=1, ntpr=100,
> > ntf=1, ntc=1, ntb=0,
> > igb=1, gbsa=1, cut=999.0, scee=1.2, extdiel=80,
> > nsnb=25, ntwx=100,
> > itgtmd=1, tgtmdfrc=0,
> > &end
> > &wt type='TGTRMSD', istep1=1, istep2=50000, value1=3.04 , value2=0.0,
> > &end
> > &wt type='END' &end
> > atoms for targeted md
> > 0.0
> > RES 1
> > END
> > END
> >
> > --
> >
> > Giulio Rastelli
> > Dipartimento di Scienze Farmaceutiche
> > Universita di Modena e Reggio Emilia
> > Via Campi 183
> > 41100 Modena - ITALY
> > -------------------------------------
> > tel 0039-059-2055145
> > fax 0039-059-2055131
> > -------------------------------------
> >
> >
>
>
>