[gmx-users] g_confrms_d options

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 5 15:47:31 CEST 2006

Arindam Ganguly wrote:
> Hi David,
> Thanks for the reply. very well i agree with what you have to say. 
> however in that case the answer  which i am getting for other options 
> claiming that the lsq fit say for backbone is 0.98732 so on ., are 
> useless values. now again if that is the case shoukld i assume that 
> native structure RMSD calculations using g_confrms_d is invalid.
> David i hope this question of mine making sense. plz clarify if i am 
> missing something important. everyone is performing rmsd calculations on 
> proteins, what is that i am doing wrong here. thanks.
> Arindam Ganguly

it will only work when you use the -name flag, but you will get nonsense 
in your case. this option is for instance for when you have two proteins 
which are very similar except for a couple of mutants.

if you are comparing apples and apples it is fine.

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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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