[gmx-users] Atom names mismatch

[George Abadir]

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