[gmx-developers] Single letter residue types in rtp files

[David van der Spoel]

Anton Feenstra wrote:
> Ranjit Vijayan wrote:
>> Of course, it is pretty straightforward for me to change the single 
>> letter residue types to two letters. But, would it not be better if 
>> the .rtp files released is set up to take care of the code's inability 
>> to handle single letter residue types or modify the above check to 
>> allow single letter residue types?
> 
> The code looks like it could have been mine (I've tried to make the name 
> matching a bit more forgiving by not insisting on a perfect match). I do 
> not think there was a good reason for excluding single-letter residue 
> names, it probably simply did not occur to me at the time how the code 
> would behave in such a situation -- and it apparently wasn't in my test 
> set... ;-{
> 
> Nevertheless, I'd think you would not want to use a building block if 
> only the first letter matched your residue name, so simply initializing 
> 'best' at 0 is not a good quick solution here...
> 
> 
Isn't it quite common to designate DNA by single letter codes as well?

That would point towards a solution that allows single letter codes anyawy..

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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