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

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 20 09:10:05 CET 2006

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 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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