AMBER Archive (2002)

Subject: Re: targeted MD

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Fri Oct 18 2002 - 10:45:33 CDT

it would help to show the output just so we can
see if sander accepted your group input and
how many atoms were selected. I believe
two residue numbers are needed for the RES command.
give it the final residue number for the range:

RES 1 124
END
END

also, if you don't use a non-zero force constant it
will calculate the RMSD but you will have no
restraint force.
Carlos

----- 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
> -------------------------------------
>
>