RE: AMBER: leaprc.ff02polEP.r1into xleap

From: Ross Walker <>
Date: Thu, 29 Nov 2007 07:54:13 -0800

Hi Denis,
You likely have a poor starting structure - I suspect two atoms are
overlapping causing a very high energy and force. Search for vlimit on the
amber mailing list archive ( and you will
find a number of suggestions for things to do. Take a look at the
minimization output - are any values particularly high - especially VDW?
Look at the atom listed as having GMAX - then look at that atom visually.
Also you can set ntwx=1 and run about 10 steps of MD and then visualize it
and you should be able to see where the "blow up" of your system originates
from - you will then need to fix your input structure.
I will reiterate Dave's comment as well. If you are new to Amber and MD
which it appears you are you should NOT be attempting to do polarizable
simulations until you are fully familiar with all the intricacies of regular
MD simulations. You should work through all of the tutorials on the amber
website and then setup and run your current system using FF99SB and make
sure you can do this first.
You should also get yourself a good book on MD and read it to make sure you
are familiar with the theory.
All the best

|\oss Walker

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From: [] On Behalf Of
Denis Courtier
Sent: Thursday, November 29, 2007 03:02
Subject: Re: AMBER: leaprc.ff02polEP.r1into xleap

Thank you David and Ross.

I have followed your recommendations. But, I got another error. Now, it is
in md step. The error in my output file is:

vlimit exceeded for step 5; vmax = 36.3511
vlimit exceeded for step 6; vmax = **********

     Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 0 9 8 9

     Note: This is usually a symptom of some deeper
     problem with the energetics of the system.

My input files, for minimization and md, are:

Initial min-n
  imin=1, maxcyc=2500, ncyc=1000,
  cut=8.0, ntb=1,ntc=2,ntf=2

300K constant temp MD
  imin=0, ntb=1
  cut=8.0, ntc=2, ntf=2,
  tempi=300.0, temp0=300.0,
  ntt=3, gamma_ln=1.0,
  nstlim=520000, dt=0.002,
  ntpr=50, ntwx=50,

Can anybody help me? How can i control vlimit? Where is the origin of my
problem? Does i have to change the ensemble?

Thank you in advance.


On Nov 28, 2007 6:58 PM, David A. Case <> wrote:

On Wed, Nov 28, 2007, Denis Courtier wrote:
> > napro=loadpdb napro.pdb
> Loading PDB file: ./napro.pdb
> Warning: name change in pdb file residue 1 ;
> this residue is split into ACE and PRO.
> 1 residues had naming warnings.
> There are split residues;
> residue sequence numbers will not correspond to those in the pdb.
> Created a new atom named: C10 within residue: .R<ACE 1>
> Created a new atom named: C11 within residue: .R<ACE 1>


The atom names in your pdb file must match those in the library.

Since it appears you are new to Amber, I would strongly recommend that you
gain experience with non-polarizable simulations before trying polarizable


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Received on Sun Dec 02 2007 - 06:07:20 PST
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