[gmx-users] Atom names mismatch

[George Abadir]

Thank you very much for your reply. Actually I ran the whole simulations 
(1000000 time steps), and the system did not crash. The molecule still 
has the structure of phenylalanine. Does this mean that the final 
coordinates are ok, or should I redo the simulation again after 
resorting the atoms.
Thanks alot,
Regards,
George

chris.neale at utoronto.ca wrote:

> This is a bona fide problem. The topology (and the names/parameters  
> for atoms) is taken from the .top file so you appear to be specifying  
> carbon coordinates for a hydrogen in the first warning and then it  
> goes from there. It is only a warning because sometimes you want to 
> be  able to work through this (e.g. if you build your .top with one 
> water  model and your .pdb has another).
>
> "does this affect the correctness and the accuracy of the results?"
>
> Yes. you have some problem that will likely lead to a crash within  
> minutes of starting the run, and even if it somehow doesn't then 
> still  you are doing something that you don't intend to.
>
> Look into your .top or just run it with mdrun for 1 step and look at  
> the output .gro in vmd. If you can't solve it then post your .top and  
> a relevant snip of your .pdb (but do try to solve it yourself).
>
> Chris.
>
> -- original message --
>
> Hi,
>      I am performing simulations with carbon nanotubes and dimers of
> phenylalanine. I got an error in the log file:"Warning: atom names in
> cnt.top and cnt_box_solvated.pdb don't match (H1 - CA)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match 
> (H2 - C)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match 
> (H3 - O)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CA
> - CB)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HA
> - CG)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CB
> - CD1)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HB1
> - CD2)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HB2
> - CE1)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CG
> - CE2)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CD1
> - CZ)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HD1
> - HA)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CE1
> - HB1)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HE1
> - HB2)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CZ
> - HD1)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HZ
> - HD2)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CE2
> - HE1)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (CD2
> - HZ)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (HD2
> - H1)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (C 
> - H2)
> Warning: atom names in cnt.top and cnt_box_solvated.pdb don't match (O 
> - H3)
> (more than 20 non-matching atom names)
> WARNING 1 [file "cnt.top", line 21]:
>   38 non-matching atom names
>   atom names from cnt.top will be used
>   atom names from cnt_box_solvated.pdb will be ignored"
>
> As far as I understand, this means that the order of the atoms in the
> topology file and the coordinate file is different. I find that this is
> just a warning and not an error. So, my question is: does this affect
> the correctness and the accuracy of the results, or the results are
> correct regardless of this warning.
>
> Thank you very much,
> Regards,
> George
>
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