AMBER Archive (2009)

Subject: Re: [AMBER] LES and NEB problem

From: Rima Chaudhuri (rima.chaudhuri_at_gmail.com)
Date: Thu Oct 15 2009 - 11:50:08 CDT

Hi!
LES: I tried using the mdin from $AMBERHOME/test/LES and this fails with the
same message as well: LES requires numextra=0
I've used AMBER ff03.

NEB: The run dies even if ineb=0. It reports the same "Could not find cntrl
namelist" error.

thanks,

On Wed, Oct 14, 2009 at 9:14 AM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> see below
>
>
> On Tue, Oct 13, 2009 at 3:35 PM, Rima Chaudhuri <rima.chaudhuri_at_gmail.com
> >wrote:
>
> > Hello!
> >
> > LES:
> > I am trying to run LES on a small part of my system (4 residue long loop)
> > using Amber10. I prepared the necessary input files using addles.
> > file rprm name=(X_solv.top) read
> > file rcvb name=(X_solv_nve6.rst) read
> > file wprm name=(les.parmtop) wovr
> > file wcrd name=(les.crd) wovr
> > action
> > omas
> > spac numc=5 pick #mon 191 194 done
> > *EOD
> >
> > sander.LES.MPI starts and then dies with the following message in the
> .out
> > file: Please find the file attached.
> > MPI Timing options:
> > profile_mpi = 0
> > LES requires numextra=0
> >
> >
> is this message relevant? which force field are you using?
>
>
>
> > I've attached the input file, md_nve2les.in, as well. Any help in
> helping
> > me
> > understand why this is happening will be much appreciated.
> >
> > NEB:
> > I am doing a NEB exercise as well. Here, I am working with just the loop
> > residues (open as structure 1 and closed as structure 2). I created
> > 30copies
> > of every atom in the loop. Addles created the needed top and crd files
> > successfully.
> >
> > Please find the details of the input file below. Here, the run dies
> giving
> > the message: "Could not find cntrl namelist".
> >
>
> does the same input work if you set ineb=0?
>
>
>
> > &cntrl
> > imin = 0, irest = 0,
> > ntc=1, ntf=1,
> > ntpr=50, ntwx=500,
> > ntb = 0, cut = 999.0, rgbmax=999.0,
> > igb = 1, saltcon=0.2,
> > nstlim = 40000, nscm=0,
> > dt = 0.0005,
> > ntt = 3, gamma_ln=1000.0,
> > tempi=0, temp0=300,
> > ineb = 1,skmin = 10,skmax = 10,
> > nmropt=1,
> > /
> > &wt type='TEMP0', istep1=0,istep2=35000,
> > value1=0.0, value2=300.0,
> > /
> > &wt type='END'
> >
> >
> > Thanks!
> >
> > --
> > -Rima
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
-Rima
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber