[gmx-users] Re: deleting duplicating atoms

[Anton Feenstra]

Lakshmi Padmavathi wrote:
> Dear Dr.feenstra,
>      you helped me many times. thank you very much. i hope you only yould help 
> for my problem.
> 
>       i am using a protein with special residues. that special residue 
> contained one N=O group, in ring. i would like to use ffG43b1 because i want 
> to make stimulation in vaccum.
> 
> but the pdb2gmx program says that
> 
> deleting duplicating atoms    O
> 
> after that again it said O1 not found ( atom name O1).

You should be aware that pdb2gmx translates several atom names in order
to understand some of the common naming conventions found in pdb files.
These are read from share/top/xlateat.dat
Entries are per line, the first word specifying a residue name, or 'Protein'
for any of the aa's from aminoacid.dat, the second word specifies the 'old'
atom name, and the third word the 'new' name. So, for example, line 9
specifies that in 'protein' atoms named 'O1' should be re-named 'O'.
That would explain why your 'O1' is deleted, because after renaming it
will have the same name as the (backbone) 'O'. You could fix this by
removing this line from xlateat.dat (you can do that in a local copy),
assuming that your input .pdb file doesn't contain other O1 atoms that
*should* be renamed.

By the way, I prefer if you ask Gromacs-related questions through the
gmx-users list. That way, questions and answers will be archived, and
possibly others could answer your question better and/or faster that I do...


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Room P275  Tel: +31 20 44 47608  Fax: +31 20 44 47610 |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "Everybody is Smashing Things Down" (Offspring)       |
|_____________|_______________________________________________________|