AMBER Archive (2009)

Subject: Re: [AMBER] LES and NEB problem

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Oct 15 2009 - 13:09:14 CDT

Sander is not finding &cntrl in your input file. If it's on the top line,
try putting a blank line above it (or any random comment). I believe each
input requires a 'title line', and if &cntrl appears at the top it may be
taking that as the title (and you want it to take that line as input!).

Best of luck!
Jason

On Thu, Oct 15, 2009 at 1:53 PM, Rima Chaudhuri <rima.chaudhuri_at_gmail.com>wrote:

> Yes, the test cases work fine.
>
> On Thu, Oct 15, 2009 at 11:54 AM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
> > do the test cases work?
> >
> > On Thu, Oct 15, 2009 at 12:50 PM, Rima Chaudhuri
> > <rima.chaudhuri_at_gmail.com>wrote:
> >
> > > 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
> > > > >
> > > > > _______________________________________________
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> > > > > AMBER_at_ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > >
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> > > >
> > >
> > >
> > >
> > > --
> > > -Rima
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>
>
>
> --
> -Rima
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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