AMBER Archive (2007)

Subject: Re: AMBER: leaprc.ff02polEP.r1into xleap

From: Denis Courtier (amber982_at_gmail.com)
Date: Thu Nov 29 2007 - 05:01:38 CST

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
 &cntrl
  ipol=1
  imin=1, maxcyc=2500, ncyc=1000,
  cut=8.0, ntb=1,ntc=2,ntf=2
/
  and

300K constant temp MD
 &cntrl
  ipol=1
  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.

Denis.

On Nov 28, 2007 6:58 PM, David A. Case <case_at_scripps.edu> 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>
>
> etc.
>
> 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
> ones.
>
> ...dac
>
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