From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Oct 27 2010 - 09:27:06 CDT
HI Axel,
Thank you very much for your reply. Yes, I want to run a simulation
with missing residues as there is no template available for these
residues.
The simulation is running fine during minimization steps and only
giving mew following messages.. which is killing NAMD when I am
increasing temperature slowly.
Warning during minimization :
Warning: Bad global exclusion count, possible error!
Warning: Increasing cutoff during minimization may avoid this.
Warning: Bad global bond count!
Warning: Bad global angle count!
Warning: Bad global dihedral count!
Warning: Bad global improper count!
ERROR during equilibration:
TCL: Setting parameter langevinTemp to 10
TCL: Running for 100 steps
ERROR: Constraint failure in RATTLE algorithm for atom 592!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 168!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 620!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 2610!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
Any help.
Thank you very much for your time.
S
>> 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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