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.
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
