[gmx-users] Gromacs tools mistakenly change the name of atoms in coordinate files

Yang Ye leafyoung at yahoo.com
Wed Jun 13 20:58:40 CEST 2007

On 6/14/2007 1:14 AM, Erik Lindahl wrote:
> Hi Robert,
> On Jun 13, 2007, at 6:48 PM, Robert Johnson wrote:
>> These are all fine points. However, the question I'm asking is why do
>> Gromacs tools change atoms named OXT in PDB files to O2? Of course
>> there are always workarounds i.e. just simply change the atom name in
>> the coordinate file. However, I was wondering if anyone knew why this
>> happened. I suppose I will submit a bugzilla.
> Don't bother for now :-)
> This is because of a few old brain-dead choices in pdb2gmx, but we're 
> working on replacing that completely, and then we'll be name-agnostic.
> The only thing I can say in our defense is that most other programs 
> also push their own naming convention when generation hydrogens, etc. 
> For instance, charmm will rename the resname of the first/last few 
> atoms in each chain to NTER/CTER.
Hi, Robert

I am clueless why this topic has again made people upset about Gromacs. 
You may search for "David Mathog" in mailing list archive.
e.g. http://www.gromacs.org/pipermail/gmx-users/2006-February/020087.html
David, in the end, contributed some conversion script you might take a look.

I admit that it is frustrated to add on more rules when I want to let 
pdb2gmx pass my PDB file. But when you are working with different force 
field, AMBER, CHARMM and OPLS-AA, like me, pdb2gmx will definitely have 
a dilemma to choose which atom instead of a fixed answer. Since, as you 
say, it is easy to change the atom name, why don't you do yourself? 
IMHO, it is rather to have a strict program which is faithful and rigid 
than to have an "smart" one which may induce errors. Of course, I 
believe Erik has a better idea to solve this problem.
> Cheers,
> Erik
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