[gmx-users] Terminus Atoms genrestr?

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 11 21:50:09 CET 2011

Teemu Murtola wrote:
> Hi,
> On Fri, Feb 11, 2011 at 21:05, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> I don't know of any Gromacs tool (other than pdb2gmx) that is smart enough
>> to determine terminal residues on its own.  If you have multiple copies of
>> the same molecule, then you know how many atoms are in each, so you can
>> script a little loop that will do it for you, otherwise I don't think
>> there's anything that will do this job on its own.  Maybe g_select, but its
>> capabilities and syntax are not yet well-documented.
> If your terminal residues have some atoms that are not present in any
> other residues (e.g., OXT could be such an atom name), you can try to
> achieve what you want with g_select with a selection like (for alpha
> carbons of the terminal residues)
>   name CA and same residue as name OXT
> @Justin: If you have concrete suggestions on how the documentation
> could be improved, I would be happy to hear them, and consider them
> when I have time to think about the documentation.  I do agree that
> it's not perfect, and this has been, in part, a conscious decision.
> This is because g_select can really make use of only part of the
> capabilities of the selection syntax, and currently there are no other
> tool that uses selections at all.  Writing a complete documentation of
> the selection syntax would require writing a lot of text that would
> have very little use in the present version, and could just serve to
> confuse people more.  Partial documentation that would only cover
> g_select would probably need to be largely rewritten to cover
> everything later, so this has not been very high on the priority list
> either.  Still, the only critique I've heard so far (from several
> people, it seems) is a vague "the documentation sucks", which doesn't
> really help in improving things, or even figuring out where people
> face problems.  g_select does provide some on-line help (by typing
> "help" in the selection prompt), which should at least briefly
> describe the syntax.

I didn't mean for that comment to be a criticism at all, and I'm sorry that it 
came off that way.  I know there are many users who (as we've seen on the list 
in the past) wish that g_select was magic and they treat it as such, so I simply 
meant it as a caution that some time investment would be necessary to make 
proper use of the program.  I certainly know you're busy doing very important 
things for Gromacs development and we all appreciate that.  Looking through the 
recent source I can tell that a lot of effort has gone into improving 
everything, in general.

One thing that I always hope to help with is documentation and learning 
material, and as such, I am trying to explore some of the new features and tools 
and hopefully I can help in maintaining this stuff, as well.

Hopefully I'll have some concrete suggestions in the future, and I certainly 
didn't mean to imply that anything sucks :)


> BR,
> Teemu


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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