From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Oct 24 2010 - 18:10:13 CDT
On Fri, Oct 22, 2010 at 4:46 PM, snoze pa <snoze.pa_at_gmail.com> wrote:
> Dear Name users,
>
> I am trying to run a namd simulation using a model pdb structure.
> Some of the residues in my Model PDB file are missing.. When I run
so do you intentionally want to run a simulation without them?
have you throught about reconstructing them?
> NAMD, the I get error message for the residue just before the missing
> residues. ERROR:
>
> Constraint failure in RATTLE algorithm for atom 99!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 148!
> ERROR: Constraint failure; simulation has become unstable.
this is an indication of a structure with very large forces
and/or velocities, which in turn is likely the result of a
bad input structure or model.
impossible to tell what exactly to do.
>
> I will highly appreciate your help.
>
> Thank you
>
> S
>
> ps: There is no error message from VMD when creating psf and pdb files.
this is doesn't say anything. VMD is (deliberately) a very stupid program.
it does what you tell it to do. whether that is correct or not, is up to you
to decide, not VMD. all it can check for are some simple consistency tests.
>
>
cheers,
axel.
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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