[gmx-users] Atom names mismatch

[chris.neale at utoronto.ca]

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